RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-09 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:17:06 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_144 python-lpbuildd_144 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 26 Jun 19:07:14 ntpdate[1798]: adjust time server 10.211.37.1 offset -0.000087 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12808202', '/home/buildd/filecache-default/e3a0751dad18cad81698aa46cb02fd9a2acf7c0b'] Unpacking chroot for build PACKAGEBUILD-12808202 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12808202'] Mounting chroot for build PACKAGEBUILD-12808202 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12808202', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-12808202 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12808202', 'amd64'] Updating debian chroot for build PACKAGEBUILD-12808202 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 Packages [1170 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [567 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe amd64 Packages [8267 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4756 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 Packages [79.5 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [34.6 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe amd64 Packages [143 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [81.5 kB] Fetched 15.7 MB in 6s (2483 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https bash binutils bsdutils ca-certificates cpp-6 debianutils dmsetup dpkg dpkg-dev findutils g++-6 gcc-6 gcc-6-base init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libcc1-0 libcilkrts5 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libip4tc0 libitm1 libkmod2 libkrb5-26-heimdal libldap-2.4-2 libldap-common liblsan0 libmount1 libmpx2 libnpth0 libperl5.24 libpng16-16 libquadmath0 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount openssl passwd perl perl-base perl-modules-5.24 systemd systemd-sysv tzdata util-linux 83 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 53.3 MB of archives. After this operation, 629 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main amd64 debianutils amd64 4.8.1.1 [85.6 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main amd64 bash amd64 4.4-5ubuntu1 [625 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main amd64 bsdutils amd64 1:2.29-1ubuntu3 [55.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg amd64 1.18.24ubuntu1 [1140 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 findutils amd64 4.6.0+git+20170606-2 [293 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main amd64 login amd64 1:4.2-3.2ubuntu2 [304 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main amd64 util-linux amd64 2.29-1ubuntu3 [913 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main amd64 mount amd64 2.29-1ubuntu3 [130 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libperl5.24 amd64 5.24.1-4ubuntu1 [3460 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 perl amd64 5.24.1-4ubuntu1 [219 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 perl-base amd64 5.24.1-4ubuntu1 [1343 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 perl-modules-5.24 all 5.24.1-4ubuntu1 [2663 kB] Get:13 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init-system-helpers all 1.48 [37.8 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-7-base amd64 7.1.0-7ubuntu1 [18.5 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main amd64 libgcc1 amd64 1:7.1.0-7ubuntu1 [39.3 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main amd64 libstdc++6 amd64 7.1.0-7ubuntu1 [403 kB] Get:17 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libapt-pkg5.0 amd64 1.4.6 [783 kB] Get:18 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt amd64 1.4.6 [1096 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main amd64 libip4tc0 amd64 1.6.0+snapshot20161117-6ubuntu1 [19.4 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main amd64 libapparmor1 amd64 2.11.0-2ubuntu8 [29.8 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main amd64 libaudit-common all 1:2.6.6-1ubuntu2 [4626 B] Get:22 http://ftpmaster.internal/ubuntu artful/main amd64 libaudit1 amd64 1:2.6.6-1ubuntu2 [37.6 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main amd64 libselinux1 amd64 2.6-3build1 [67.5 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main amd64 libsemanage-common all 2.6-2build1 [6738 B] Get:25 http://ftpmaster.internal/ubuntu artful/main amd64 libsemanage1 amd64 2.6-2build1 [82.2 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main amd64 passwd amd64 1:4.2-3.2ubuntu2 [781 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main amd64 libuuid1 amd64 2.29-1ubuntu3 [14.8 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main amd64 libblkid1 amd64 2.29-1ubuntu3 [110 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main amd64 libgcrypt20 amd64 1.7.7-2 [400 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main amd64 libkmod2 amd64 24-1ubuntu1 [39.9 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main amd64 libmount1 amd64 2.29-1ubuntu3 [119 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main amd64 systemd amd64 233-8ubuntu1 [2440 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main amd64 libsystemd0 amd64 233-8ubuntu1 [210 kB] Get:34 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init amd64 1.48 [5806 B] Get:35 http://ftpmaster.internal/ubuntu artful/main amd64 systemd-sysv amd64 233-8ubuntu1 [12.7 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main amd64 libfdisk1 amd64 2.29-1ubuntu3 [145 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main amd64 libsmartcols1 amd64 2.29-1ubuntu3 [69.4 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main amd64 libudev1 amd64 233-8ubuntu1 [56.9 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main amd64 libdevmapper1.02.1 amd64 2:1.02.137-2ubuntu2 [135 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main amd64 dmsetup amd64 2:1.02.137-2ubuntu2 [71.8 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main amd64 libroken18-heimdal amd64 7.1.0+dfsg-13 [40.8 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main amd64 libasn1-8-heimdal amd64 7.1.0+dfsg-13 [176 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main amd64 libtasn1-6 amd64 4.12-2 [35.6 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main amd64 libgnutls30 amd64 3.5.8-6ubuntu1 [675 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main amd64 libheimbase1-heimdal amd64 7.1.0+dfsg-13 [29.1 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main amd64 libhcrypto4-heimdal amd64 7.1.0+dfsg-13 [88.1 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main amd64 libwind0-heimdal amd64 7.1.0+dfsg-13 [47.9 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main amd64 libhx509-5-heimdal amd64 7.1.0+dfsg-13 [107 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main amd64 libsqlite3-0 amd64 3.16.2-5 [486 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main amd64 libkrb5-26-heimdal amd64 7.1.0+dfsg-13 [206 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main amd64 libheimntlm0-heimdal amd64 7.1.0+dfsg-13 [15.1 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main amd64 libgssapi3-heimdal amd64 7.1.0+dfsg-13 [97.5 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5ubuntu1 [155 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main amd64 libldap-common all 2.4.44+dfsg-5ubuntu1 [17.5 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main amd64 libnpth0 amd64 1.5-2 [7622 B] Get:56 http://ftpmaster.internal/ubuntu artful/main amd64 libssl1.0.0 amd64 1.0.2g-1ubuntu13 [1081 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main amd64 tzdata all 2017b-2 [203 kB] Get:58 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt-transport-https amd64 1.4.6 [34.2 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main amd64 openssl amd64 1.0.2g-1ubuntu13 [491 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main amd64 ca-certificates all 20161130+nmu1 [186 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main amd64 libpng16-16 amd64 1.6.29-3 [173 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main amd64 advancecomp amd64 2.0-1 [198 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main amd64 binutils amd64 2.28-6ubuntu1 [2435 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main amd64 libquadmath0 amd64 7.1.0-7ubuntu1 [132 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main amd64 libitm1 amd64 7.1.0-7ubuntu1 [27.6 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main amd64 libmpx2 amd64 7.1.0-7ubuntu1 [11.7 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main amd64 liblsan0 amd64 7.1.0-7ubuntu1 [126 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main amd64 libtsan0 amd64 7.1.0-7ubuntu1 [275 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main amd64 libubsan0 amd64 7.1.0-7ubuntu1 [119 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main amd64 libcilkrts5 amd64 7.1.0-7ubuntu1 [42.3 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main amd64 libgomp1 amd64 7.1.0-7ubuntu1 [76.3 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main amd64 libatomic1 amd64 7.1.0-7ubuntu1 [8900 B] Get:73 http://ftpmaster.internal/ubuntu artful/main amd64 libasan3 amd64 6.3.0-19ubuntu1 [314 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main amd64 g++-6 amd64 6.3.0-19ubuntu1 [7393 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main amd64 libstdc++-6-dev amd64 6.3.0-19ubuntu1 [1409 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-6 amd64 6.3.0-19ubuntu1 [7216 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main amd64 libgcc-6-dev amd64 6.3.0-19ubuntu1 [2308 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main amd64 libcc1-0 amd64 7.1.0-7ubuntu1 [38.5 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main amd64 cpp-6 amd64 6.3.0-19ubuntu1 [6605 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-6-base amd64 6.3.0-19ubuntu1 [17.4 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main amd64 libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main amd64 libusb-0.1-4 amd64 2:0.1.12-31 [17.1 kB] Get:84 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 linux-libc-dev amd64 4.11.0-8.13 [923 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.3 MB in 2s (20.5 MB/s) (Reading database ... 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Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12808202', 'amd64', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=artful-proposed', '--purge=never', '--nolog', '-A', 'python-pysam_0.10.0+ds-2build2.dsc'] Initiating build PACKAGEBUILD-12808202 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:17:06 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-09.buildd +==============================================================================+ | python-pysam 0.10.0+ds-2build2 (amd64) 26 Jun 2017 19:08 | +==============================================================================+ Package: python-pysam Version: 0.10.0+ds-2build2 Source Version: 0.10.0+ds-2build2 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/python-pysam-5YgBdr/python-pysam-0.10.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-5YgBdr' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12808202/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.10.0+ds-2build2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-czSjCG/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-czSjCG/apt_archive ./ InRelease Get:2 copy:/<>/resolver-czSjCG/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-czSjCG/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-czSjCG/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-czSjCG/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (105 kB/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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-czSjCG/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (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 ... 12505 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) ... Merged Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose Filtered Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-VDcpTU/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-VDcpTU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-VDcpTU/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-VDcpTU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-VDcpTU/apt_archive ./ Sources [299 B] Get:5 copy:/<>/resolver-VDcpTU/apt_archive ./ Packages [618 B] Fetched 3036 B in 0s (141 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-pysam 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 bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts2 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-dev python3.6-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python-coverage python-nose-doc python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.5-venv python3.5-doc python3.6-venv python3.6-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 packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts2 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-dev python3.6-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 87 newly installed, 1 to remove and 0 not upgraded. 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Setting up python (2.7.13-2) ... Setting up libpython3.6:amd64 (3.6.2~rc1-1) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-3) ... Setting up libpython3-stdlib:amd64 (3.5.3-1ubuntu3) ... Setting up libpython-dev:amd64 (2.7.13-2) ... Setting up python3.6 (3.6.2~rc1-1) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:amd64 (3.5.3-3) ... Setting up python-dev (2.7.13-2) ... Setting up libpython-all-dev:amd64 (2.7.13-2) ... Setting up python-pkg-resources (36.0.1-1) ... Setting up libpython3.6-dev:amd64 (3.6.2~rc1-1) ... Setting up libpython3.5-dev:amd64 (3.5.3-3) ... Setting up cython (0.25.2-1build1) ... Setting up python3.6-dev (3.6.2~rc1-1) ... Setting up python3.5-dev (3.5.3-3) ... Setting up python-nose (1.3.7-2) ... Setting up python-all (2.7.13-2) ... Setting up libpython3-dev:amd64 (3.5.3-1ubuntu3) ... Setting up python-setuptools (36.0.1-1) ... Setting up python-all-dev (2.7.13-2) ... Setting up libpython3-all-dev:amd64 (3.5.3-1ubuntu3) ... Setting up dh-autoreconf (14) ... Setting up python3 (3.5.3-1ubuntu3) ... Setting up python3-dev (3.5.3-1ubuntu3) ... Setting up python3-pkg-resources (36.0.1-1) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up python3-nose (1.3.7-2) ... Setting up python3-all (3.5.3-1ubuntu3) ... Setting up cython3 (0.25.2-1build1) ... Setting up python3-setuptools (36.0.1-1) ... Setting up dh-python (2.20170125) ... Setting up debhelper (10.4ubuntu3) ... Setting up python3-all-dev (3.5.3-1ubuntu3) ... Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ... (Reading database ... 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Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-81-generic amd64 (x86_64) Toolchain package versions: binutils_2.28-6ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.3.0-19ubuntu1 gcc-6_6.3.0-19ubuntu1 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-19ubuntu1 libstdc++6_7.1.0-7ubuntu1 linux-libc-dev_4.11.0-8.13 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.4.6 apt-transport-https_1.4.6 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu99 base-passwd_3.5.43 bash_4.4-5ubuntu1 bcftools_1.4.1-1 binutils_2.28-6ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-19ubuntu1 cython_0.25.2-1build1 cython3_0.25.2-1build1 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.4ubuntu3 debianutils_4.8.1.1 dh-autoreconf_14 dh-python_2.20170125 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20170606-2 g++_4:6.3.0-2ubuntu1 g++-6_6.3.0-19ubuntu1 gcc_4:6.3.0-2ubuntu1 gcc-6_6.3.0-19ubuntu1 gcc-6-base_6.3.0-19ubuntu1 gcc-7-base_7.1.0-7ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.48 init-system-helpers_1.48 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu8 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1 libasan3_6.3.0-19ubuntu1 libasn1-8-heimdal_7.1.0+dfsg-13 libassuan0_2.4.3-2 libatomic1_7.1.0-7ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.6.6-1ubuntu2 libaudit1_1:2.6.6-1ubuntu2 libblkid1_2.29-1ubuntu3 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9ubuntu2 libc-dev-bin_2.24-9ubuntu2 libc6_2.24-9ubuntu2 libc6-dev_2.24-9ubuntu2 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-7ubuntu1 libcilkrts5_7.1.0-7ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu2 libdpkg-perl_1.18.24ubuntu1 libexpat1_2.2.1-2 libexpat1-dev_2.2.1-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu3 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.035-2 libgcc-6-dev_6.3.0-19ubuntu1 libgcc1_1:7.1.0-7ubuntu1 libgcrypt20_1.7.7-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu1 libgomp1_7.1.0-7ubuntu1 libgpg-error0_1.26-2 libgsl2_2.3+dfsg-1 libgssapi-krb5-2_1.15-2 libgssapi3-heimdal_7.1.0+dfsg-13 libhcrypto4-heimdal_7.1.0+dfsg-13 libheimbase1-heimdal_7.1.0+dfsg-13 libheimntlm0-heimdal_7.1.0+dfsg-13 libhogweed4_3.3-1 libhts-dev_1.4.1-2ubuntu1 libhts2_1.4.1-2ubuntu1 libhx509-5-heimdal_7.1.0+dfsg-13 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0+snapshot20161117-6ubuntu1 libisl15_0.18-1 libitm1_7.1.0-7ubuntu1 libk5crypto3_1.15-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-13 libkrb5-3_1.15-2 libkrb5support0_1.15-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-5ubuntu1 libldap-common_2.4.44+dfsg-5ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblsan0_7.1.0-7ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29-1ubuntu3 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libmpx2_7.1.0-7ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-3 libperl5.24_5.24.1-4ubuntu1 libpipeline1_1.4.1-2 libpng16-16_1.6.29-3 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libpython-all-dev_2.7.13-2 libpython-dev_2.7.13-2 libpython-stdlib_2.7.13-2 libpython2.7_2.7.13-2 libpython2.7-dev_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-all-dev_3.5.3-1ubuntu3 libpython3-dev_3.5.3-1ubuntu3 libpython3-stdlib_3.5.3-1ubuntu3 libpython3.5_3.5.3-3 libpython3.5-dev_3.5.3-3 libpython3.5-minimal_3.5.3-3 libpython3.5-stdlib_3.5.3-3 libpython3.6_3.6.2~rc1-1 libpython3.6-dev_3.6.2~rc1-1 libpython3.6-minimal_3.6.2~rc1-1 libpython3.6-stdlib_3.6.2~rc1-1 libquadmath0_7.1.0-7ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-13 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build1 libsemanage-common_2.6-2build1 libsemanage1_2.6-2build1 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu3 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.3.0-19ubuntu1 libstdc++6_7.1.0-7ubuntu1 libsystemd0_233-8ubuntu1 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_7.1.0-7ubuntu1 libubsan0_7.1.0-7ubuntu1 libudev1_233-8ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu3 libwind0-heimdal_7.1.0+dfsg-13 libxml2_2.9.4+dfsg1-2.2ubuntu1 linux-libc-dev_4.11.0-8.13 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu2 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu3 multiarch-support_2.24-9ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu2 patch_2.7.5-1build1 perl_5.24.1-4ubuntu1 perl-base_5.24.1-4ubuntu1 perl-modules-5.24_5.24.1-4ubuntu1 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-minimal_2.7.13-2 python-nose_1.3.7-2 python-pkg-resources_36.0.1-1 python-setuptools_36.0.1-1 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1ubuntu3 python3-all_3.5.3-1ubuntu3 python3-all-dev_3.5.3-1ubuntu3 python3-dev_3.5.3-1ubuntu3 python3-minimal_3.5.3-1ubuntu3 python3-nose_1.3.7-2 python3-pkg-resources_36.0.1-1 python3-setuptools_36.0.1-1 python3.5_3.5.3-3 python3.5-dev_3.5.3-3 python3.5-minimal_3.5.3-3 python3.6_3.6.2~rc1-1 python3.6-dev_3.6.2~rc1-1 python3.6-minimal_3.6.2~rc1-1 readline-common_7.0-0ubuntu2 samtools_1.4.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-8ubuntu1 systemd-sysv_233-8ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.4.1-2ubuntu1 tar_1.29b-1.1 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu3 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Jun 26 07:29:53 2017 UTC gpgv: using RSA key gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.10.0+ds-2build2.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.10.0+ds dpkg-source: info: unpacking python-pysam_0.10.0+ds.orig.tar.gz dpkg-source: info: unpacking python-pysam_0.10.0+ds-2build2.debian.tar.xz dpkg-source: info: applying rpath.patch dpkg-source: info: applying htslib-external-config.patch dpkg-source: info: applying exclude_test_tyring_to_access_remote_ftpserver.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/python-pysam-0.10.0+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/python-pysam-0.10.0+ds' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.10.0+ds-2build2 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build python-pysam-0.10.0+ds dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi dh clean --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' dh_auto_clean I: pybuild base:184: python2.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:184: python3.6 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it I: pybuild base:184: python3.5 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.5' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.6 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.5 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/version.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c building 'pysam.libchtslib' extension creating build creating build/temp.linux-amd64-2.7 creating build/temp.linux-amd64-2.7/pysam x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-amd64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libchtslib.o build/temp.linux-amd64-2.7/pysam/htslib_util.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c building 'pysam.libcsamfile' extension creating build/temp.linux-amd64-2.7/samtools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-amd64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-amd64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-amd64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcsamfile.o build/temp.linux-amd64-2.7/pysam/htslib_util.o build/temp.linux-amd64-2.7/pysam/samfile_util.o build/temp.linux-amd64-2.7/samtools/kprobaln.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-amd64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-amd64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-amd64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcalignmentfile.o build/temp.linux-amd64-2.7/pysam/htslib_util.o build/temp.linux-amd64-2.7/pysam/samfile_util.o build/temp.linux-amd64-2.7/samtools/kprobaln.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-amd64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-amd64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-amd64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcalignedsegment.o build/temp.linux-amd64-2.7/pysam/htslib_util.o build/temp.linux-amd64-2.7/pysam/samfile_util.o build/temp.linux-amd64-2.7/samtools/kprobaln.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so cythoning pysam/libctabix.pyx to pysam/libctabix.c building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-amd64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-amd64-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libctabix.o build/temp.linux-amd64-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-amd64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libctabixproxies.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so cythoning pysam/libcvcf.pyx to pysam/libcvcf.c warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-amd64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.66’: pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcvcf.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so cythoning pysam/libcbcf.pyx to pysam/libcbcf.c building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-amd64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:28476:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5:0, from pysam/libcbcf.c:438: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcbcf.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-amd64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcbgzf.o -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-amd64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-ZZaKJ6/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so cythoning pysam/libcutils.pyx to pysam/libcutils.c building 'pysam.libcutils' extension creating build/temp.linux-amd64-2.7/bcftools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-amd64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:10530:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-amd64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-amd64-2.7/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:36:3: error: conflicting types for ‘errmod_t’ } errmod_t; ^~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:659:25: note: previous declaration of ‘errmod_t’ was here typedef struct errmod_t errmod_t; ^~~~~~~~ In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:38:11: error: conflicting types for ‘errmod_init’ errmod_t *errmod_init(double depcorr); ^~~~~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:661:11: note: previous declaration of ‘errmod_init’ was here errmod_t *errmod_init(double depcorr); ^~~~~~~~~~~ In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:39:6: error: conflicting types for ‘errmod_destroy’ void errmod_destroy(errmod_t *em); ^~~~~~~~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:662:6: note: previous declaration of ‘errmod_destroy’ was here void errmod_destroy(errmod_t *em); ^~~~~~~~~~~~~~ In file included from samtools/bam2bcf.h:31:0, from samtools/bam_tview.h:35, from samtools/bam_tview_html.c.pysam.c:30: samtools/errmod.h:47:5: error: conflicting types for ‘errmod_cal’ int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); ^~~~~~~~~~ In file included from /usr/include/htslib/sam.h:31:0, from samtools/bam_tview.h:34, from samtools/bam_tview_html.c.pysam.c:30: /usr/include/htslib/hts.h:670:5: note: previous declaration of ‘errmod_cal’ was here int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); ^~~~~~~~~~ error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 E: pybuild pybuild:283: build: plugin distutils failed with: exit code=1: /usr/bin/python setup.py build dh_auto_build: pybuild --build -i python{version} -p 2.7 returned exit code 13 debian/rules:32: recipe for target 'build' failed make: *** [build] Error 25 dpkg-buildpackage: error: debian/rules build gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170626-1911 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 66696 Build-Time: 180 Distribution: artful-proposed Fail-Stage: build Host Architecture: amd64 Install-Time: 52 Job: python-pysam_0.10.0+ds-2build2.dsc Machine Architecture: amd64 Package: python-pysam Package-Time: 234 Source-Version: 0.10.0+ds-2build2 Space: 66696 Status: attempted Version: 0.10.0+ds-2build2 -------------------------------------------------------------------------------- Finished at 20170626-1911 Build needed 00:03:54, 66696k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12808202'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12808202/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12808202'] Unmounting chroot for build PACKAGEBUILD-12808202... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12808202'] Removing build PACKAGEBUILD-12808202