https://launchpad.net/ubuntu/+source/cyvcf2/0.10.8-1/+build/16384954 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-034 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:45 UTC 2019 x86_64 Buildd toolchain package versions: launchpad-buildd_167 python-lpbuildd_167 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 13 Feb 05:08:55 ntpdate[1799]: adjust time server 10.211.37.1 offset 0.001034 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16384954 --image-type chroot /home/buildd/filecache-default/1b8bd95dfc080fb8062b439d66609df4d6cce84f Creating target for build PACKAGEBUILD-16384954 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16384954 Starting target for build PACKAGEBUILD-16384954 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16384954 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-16384954 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16384954 Updating target for build PACKAGEBUILD-16384954 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 Packages [985 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe i386 Packages [9110 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5254 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main i386 Packages [42.2 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [22.1 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 Packages [173 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [99.3 kB] Fetched 16.7 MB in 4s (3821 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libreadline7 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-9-base libreadline8 The following packages will be upgraded: adduser apt base-passwd bash binutils binutils-common binutils-i686-linux-gnu bsdutils ca-certificates coreutils cpp-8 dash debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-8 gcc-8 gcc-8-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libapt-pkg5.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libcap-ng0 libcap2 libcc1-0 libcom-err2 libcomerr2 libcryptsetup12 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfdisk1 libgcc-8-dev libgcc1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libip4tc0 libitm1 libjson-c3 liblz4-1 liblzma5 libmount1 libmpfr6 libmpx2 libncurses6 libncursesw6 libnettle6 libperl5.28 libpng16-16 libprocps7 libquadmath0 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login lsb-base mount ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.28 pkgbinarymangler procps readline-common sed systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 106 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 67.9 MB of archives. After this operation, 8538 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main i386 debianutils i386 4.8.6.1 [85.9 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main i386 bash i386 5.0-2ubuntu1 [677 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main i386 bsdutils i386 1:2.33.1-0.1ubuntu1 [65.9 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main i386 coreutils i386 8.30-1ubuntu1 [1316 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 tar i386 1.30+dfsg-5 [265 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main i386 dpkg i386 1.19.2ubuntu2 [1124 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main i386 libperl5.28 i386 5.28.1-4 [3445 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 perl i386 5.28.1-4 [204 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 perl-base i386 5.28.1-4 [1602 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 perl-modules-5.28 all 5.28.1-4 [2811 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main i386 libdb5.3 i386 5.3.28+dfsg1-0.3 [737 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm6 i386 1.18.1-2build1 [32.0 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm-compat4 i386 1.18.1-2build1 [6708 B] Get:14 http://ftpmaster.internal/ubuntu disco/main i386 zlib1g i386 1:1.2.11.dfsg-1ubuntu2 [55.9 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 debconf all 1.5.70 [122 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 dash i386 0.5.10.2-4ubuntu1 [90.8 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 findutils i386 4.6.0+git+20190105-2 [343 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main i386 grep i386 3.3-1 [155 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main i386 gzip i386 1.9-3 [94.8 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main i386 libsmartcols1 i386 2.33.1-0.1ubuntu1 [98.7 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main i386 libuuid1 i386 2.33.1-0.1ubuntu1 [21.9 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main i386 libblkid1 i386 2.33.1-0.1ubuntu1 [147 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main i386 libfdisk1 i386 2.33.1-0.1ubuntu1 [190 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main i386 libmount1 i386 2.33.1-0.1ubuntu1 [158 kB] Get:25 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libncurses6 i386 6.1+20181013-2ubuntu1 [108 kB] Get:26 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libtinfo6 i386 6.1+20181013-2ubuntu1 [85.2 kB] Get:27 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libncursesw6 i386 6.1+20181013-2ubuntu1 [142 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main i386 fdisk i386 2.33.1-0.1ubuntu1 [126 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 login i386 1:4.5-1.1ubuntu1 [266 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main i386 util-linux i386 2.33.1-0.1ubuntu1 [1026 kB] Get:31 http://ftpmaster.internal/ubuntu disco-proposed/main i386 ncurses-bin i386 6.1+20181013-2ubuntu1 [166 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main i386 sed i386 4.7-1 [193 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main i386 libdebconfclient0 i386 0.247ubuntu1 [6504 B] Get:34 http://ftpmaster.internal/ubuntu disco/main i386 base-passwd i386 3.5.46 [47.9 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main i386 init-system-helpers all 1.56+nmu1 [38.2 kB] Get:36 http://ftpmaster.internal/ubuntu disco-proposed/main i386 ncurses-base all 6.1+20181013-2ubuntu1 [18.4 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main i386 libnettle6 i386 3.4.1-1 [128 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main i386 libhogweed4 i386 3.4.1-1 [142 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main i386 libgnutls30 i386 3.6.5-2ubuntu1 [770 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main i386 gcc-9-base i386 9-20190207-0ubuntu1 [17.2 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main i386 libgcc1 i386 1:9-20190207-0ubuntu1 [48.0 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main i386 liblz4-1 i386 1.8.3-1ubuntu1 [61.2 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main i386 liblzma5 i386 5.2.4-1 [99.7 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++6 i386 9-20190207-0ubuntu1 [545 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main i386 libudev1 i386 240-5ubuntu3 [73.1 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main i386 libzstd1 i386 1.3.8+dfsg-3 [225 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main i386 libapt-pkg5.0 i386 1.8.0~rc3 [899 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage-common all 2.8-2 [7016 B] Get:49 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage1 i386 2.8-2 [94.2 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main i386 passwd i386 1:4.5-1.1ubuntu1 [817 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main i386 adduser all 3.118ubuntu1 [163 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main i386 libgpg-error0 i386 1.35-1 [62.3 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main i386 gpgv i386 2.2.12-1ubuntu3 [217 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main i386 apt i386 1.8.0~rc3 [1239 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main i386 systemd-sysv i386 240-5ubuntu3 [9380 B] Get:56 http://ftpmaster.internal/ubuntu disco/main i386 libcap2 i386 1:2.25-2 [13.7 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main i386 libargon2-1 i386 0~20171227-0.2 [23.5 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main i386 libjson-c3 i386 0.12.1+ds-2 [24.0 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main i386 libcryptsetup12 i386 2:2.0.6-1ubuntu1 [157 kB] Get:60 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libip4tc0 i386 1.8.2-3ubuntu1 [21.5 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main i386 mount i386 2.33.1-0.1ubuntu1 [117 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main i386 systemd i386 240-5ubuntu3 [3463 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main i386 libsystemd0 i386 240-5ubuntu3 [267 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main i386 libext2fs2 i386 1.44.5-1 [186 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main i386 e2fsprogs i386 1.44.5-1 [550 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main i386 init i386 1.56+nmu1 [6076 B] Get:67 http://ftpmaster.internal/ubuntu disco/main i386 libcap-ng0 i386 0.7.9-2 [11.1 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main i386 libgomp1 i386 9-20190207-0ubuntu1 [94.4 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main i386 libitm1 i386 9-20190207-0ubuntu1 [30.7 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main i386 libatomic1 i386 9-20190207-0ubuntu1 [9716 B] Get:71 http://ftpmaster.internal/ubuntu disco/main i386 libasan5 i386 9-20190207-0ubuntu1 [409 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main i386 libubsan1 i386 9-20190207-0ubuntu1 [148 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main i386 libmpx2 i386 8.2.0-20ubuntu1 [13.0 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main i386 libquadmath0 i386 9-20190207-0ubuntu1 [230 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main i386 g++-8 i386 8.2.0-20ubuntu1 [10.1 MB] Get:76 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8 i386 8.2.0-20ubuntu1 [9868 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++-8-dev i386 8.2.0-20ubuntu1 [1592 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main i386 libgcc-8-dev i386 8.2.0-20ubuntu1 [2303 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main i386 libmpfr6 i386 4.0.2-1 [246 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main i386 libcc1-0 i386 9-20190207-0ubuntu1 [49.3 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main i386 binutils-i686-linux-gnu i386 2.32-1ubuntu4 [2008 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main i386 libbinutils i386 2.32-1ubuntu4 [509 kB] Get:83 http://ftpmaster.internal/ubuntu disco/main i386 binutils i386 2.32-1ubuntu4 [3388 B] Get:84 http://ftpmaster.internal/ubuntu disco/main i386 binutils-common i386 2.32-1ubuntu4 [200 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main i386 cpp-8 i386 8.2.0-20ubuntu1 [9003 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8-base i386 8.2.0-20ubuntu1 [18.8 kB] Get:87 http://ftpmaster.internal/ubuntu disco/main i386 libcom-err2 i386 1.44.5-1 [9708 B] Get:88 http://ftpmaster.internal/ubuntu disco/main i386 libprocps7 i386 2:3.3.15-2ubuntu2 [33.8 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main i386 libss2 i386 1.44.5-1 [11.6 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main i386 lsb-base all 10.2018112800ubuntu1 [12.6 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main i386 procps i386 2:3.3.15-2ubuntu2 [229 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main i386 ca-certificates all 20190110 [146 kB] Get:93 http://ftpmaster.internal/ubuntu disco/main i386 readline-common all 8.0-1 [53.4 kB] Get:94 http://ftpmaster.internal/ubuntu disco/main i386 libreadline8 i386 8.0-1 [133 kB] Get:95 http://ftpmaster.internal/ubuntu disco/main i386 libsqlite3-0 i386 3.26.0+fossilbc891ac6b-2 [566 kB] Get:96 http://ftpmaster.internal/ubuntu disco/main i386 tzdata all 2018i-1 [189 kB] Get:97 http://ftpmaster.internal/ubuntu disco/main i386 xz-utils i386 5.2.4-1 [87.0 kB] Get:98 http://ftpmaster.internal/ubuntu disco/main i386 libpng16-16 i386 1.6.36-5 [187 kB] Get:99 http://ftpmaster.internal/ubuntu disco/main i386 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:100 http://ftpmaster.internal/ubuntu disco/main i386 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:101 http://ftpmaster.internal/ubuntu disco/main i386 e2fslibs i386 1.44.5-1 [2704 B] Get:102 http://ftpmaster.internal/ubuntu disco/main i386 libassuan0 i386 2.5.2-1 [37.4 kB] Get:103 http://ftpmaster.internal/ubuntu disco/main i386 gpg i386 2.2.12-1ubuntu3 [514 kB] Get:104 http://ftpmaster.internal/ubuntu disco/main i386 gpgconf i386 2.2.12-1ubuntu3 [130 kB] Get:105 http://ftpmaster.internal/ubuntu disco/main i386 gpg-agent i386 2.2.12-1ubuntu3 [249 kB] Get:106 http://ftpmaster.internal/ubuntu disco/main i386 libcomerr2 i386 1.44.5-1 [2700 B] Get:107 http://ftpmaster.internal/ubuntu disco-proposed/main i386 linux-libc-dev i386 4.19.0-13.14 [1075 kB] Get:108 http://ftpmaster.internal/ubuntu disco/main i386 pkgbinarymangler all 144 [55.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 67.9 MB in 5s (14.8 MB/s) (Reading database ... 12659 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6.1_i386.deb ... Unpacking debianutils (4.8.6.1) over (4.8.6) ... Setting up debianutils (4.8.6.1) ... (Reading database ... 12659 files and directories currently installed.) Preparing to unpack .../bash_5.0-2ubuntu1_i386.deb ... Unpacking bash (5.0-2ubuntu1) over (4.4.18-2ubuntu3) ... Setting up bash (5.0-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12659 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.33.1-0.1ubuntu1_i386.deb ... Unpacking bsdutils (1:2.33.1-0.1ubuntu1) over (1:2.32-0.1ubuntu2) ... Setting up bsdutils (1:2.33.1-0.1ubuntu1) ... (Reading database ... 12659 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-1ubuntu1_i386.deb ... Unpacking coreutils (8.30-1ubuntu1) over (8.28-1ubuntu2) ... Setting up coreutils (8.30-1ubuntu1) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-16384954 i386 disco-proposed -c chroot:build-PACKAGEBUILD-16384954 --arch=i386 --dist=disco-proposed --nolog cyvcf2_0.10.8-1.dsc Initiating build PACKAGEBUILD-16384954 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:45 UTC 2019 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-034.buildd +==============================================================================+ | cyvcf2 0.10.8-1 (i386) 13 Feb 2019 05:09 | +==============================================================================+ Package: cyvcf2 Version: 0.10.8-1 Source Version: 0.10.8-1 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/cyvcf2-XM80rW/cyvcf2-0.10.8' with '<>' I: NOTICE: Log filtering will replace 'build/cyvcf2-XM80rW' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16384954/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cyvcf2_0.10.8-1.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-XpYHFf/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-XpYHFf/apt_archive ./ InRelease Get:2 copy:/<>/resolver-XpYHFf/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-XpYHFf/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-XpYHFf/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-XpYHFf/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (251 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 package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-XpYHFf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12709 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 12~), dh-python, zlib1g-dev, cython, cython3, python-all-dev, python-setuptools, python3-setuptools, python3-all-dev, python-numpy, python3-numpy, python-coloredlogs, python3-coloredlogs, python-click, python3-click, python-nose, python3-nose, libssl-dev, libcurl4-gnutls-dev | libcurl4-openssl-dev, libhts-dev, libbz2-dev Filtered Build-Depends: debhelper (>= 12~), dh-python, zlib1g-dev, cython, cython3, python-all-dev, python-setuptools, python3-setuptools, python3-all-dev, python-numpy, python3-numpy, python-coloredlogs, python3-coloredlogs, python-click, python3-click, python-nose, python3-nose, libssl-dev, libcurl4-gnutls-dev | libcurl4-openssl-dev, libhts-dev, libbz2-dev dpkg-deb: building package 'sbuild-build-depends-cyvcf2-dummy' in '/<>/resolver-UdBKrP/apt_archive/sbuild-build-depends-cyvcf2-dummy.deb'. Ign:1 copy:/<>/resolver-UdBKrP/apt_archive ./ InRelease Get:2 copy:/<>/resolver-UdBKrP/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-UdBKrP/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-UdBKrP/apt_archive ./ Sources [325 B] Get:5 copy:/<>/resolver-UdBKrP/apt_archive ./ Packages [648 B] Fetched 3092 B in 0s (287 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install cyvcf2 build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-click python-colorama python-coloredlogs python-dev python-humanfriendly python-minimal python-monotonic python-nose python-numpy python-pkg-resources python-setuptools python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-click python3-colorama python3-coloredlogs python3-dev python3-distutils python3-humanfriendly python3-lib2to3 python3-minimal python3-nose python3-numpy python3-pkg-resources python3-setuptools python3.7 python3.7-dev python3.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config krb5-doc krb5-user liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python-coverage python-nose-doc gfortran python-pytest python-numpy-dbg python-numpy-doc python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3-pytest python3-numpy-dbg python3.7-venv python3.7-doc Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-click python-colorama python-coloredlogs python-dev python-humanfriendly python-minimal python-monotonic python-nose python-numpy python-pkg-resources python-setuptools python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-click python3-colorama python3-coloredlogs python3-dev python3-distutils python3-humanfriendly python3-lib2to3 python3-minimal python3-nose python3-numpy python3-pkg-resources python3-setuptools python3.7 python3.7-dev python3.7-minimal sbuild-build-depends-cyvcf2-dummy zlib1g-dev 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 129 MB of archives. After this operation, 318 MB of additional disk space will be used. Get:1 copy:/<>/resolver-UdBKrP/apt_archive ./ sbuild-build-depends-cyvcf2-dummy 0.invalid.0 [972 B] Get:2 http://ftpmaster.internal/ubuntu disco/main i386 libpython3.7-minimal i386 3.7.2-2 [546 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main i386 libexpat1 i386 2.2.6-1 [84.8 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main i386 python3.7-minimal i386 3.7.2-2 [1694 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 python3-minimal i386 3.7.2-1 [23.5 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main i386 mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main i386 libmpdec2 i386 2.4.2-2 [80.0 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 libpython3.7-stdlib i386 3.7.2-2 [1748 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 python3.7 i386 3.7.2-2 [278 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 libpython3-stdlib i386 3.7.2-1 [7024 B] Get:11 http://ftpmaster.internal/ubuntu disco/main i386 python3 i386 3.7.2-1 [47.2 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main i386 libbsd0 i386 0.9.1-1 [48.8 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main i386 bsdmainutils i386 11.1.2ubuntu2 [183 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 groff-base i386 1.22.4-2 [880 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 libpipeline1 i386 1.5.1-2 [28.0 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 man-db i386 2.8.5-2 [1111 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main i386 libpython2.7-minimal i386 2.7.15-8 [335 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main i386 python2.7-minimal i386 2.7.15-8 [1322 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main i386 python2-minimal i386 2.7.15-4 [28.0 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main i386 python-minimal i386 2.7.15-4 [5980 B] Get:22 http://ftpmaster.internal/ubuntu disco/main i386 libpython2.7-stdlib i386 2.7.15-8 [1934 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main i386 python2.7 i386 2.7.15-8 [239 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main i386 libpython2-stdlib i386 2.7.15-4 [7592 B] Get:25 http://ftpmaster.internal/ubuntu disco/main i386 libpython-stdlib i386 2.7.15-4 [5824 B] Get:26 http://ftpmaster.internal/ubuntu disco/main i386 python2 i386 2.7.15-4 [26.5 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main i386 python i386 2.7.15-4 [7832 B] Get:28 http://ftpmaster.internal/ubuntu disco/main i386 libmagic-mgc i386 1:5.35-2 [200 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 libmagic1 i386 1:5.35-2 [80.0 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main i386 file i386 1:5.35-2 [22.8 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main i386 libelf1 i386 0.175-2 [49.9 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main i386 libglib2.0-0 i386 2.59.2-2 [1311 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main i386 libicu63 i386 63.1-6 [8435 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main i386 libxml2 i386 2.9.4+dfsg1-7ubuntu3 [658 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main i386 gettext-base i386 0.19.8.1-9 [51.2 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main i386 libkrb5support0 i386 1.17-1 [36.2 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main i386 libk5crypto3 i386 1.17-1 [90.0 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main i386 libkeyutils1 i386 1.6-2 [11.0 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main i386 libkrb5-3 i386 1.17-1 [357 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main i386 libgssapi-krb5-2 i386 1.17-1 [132 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main i386 libpsl5 i386 0.20.2-2 [50.7 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main i386 libsigsegv2 i386 2.12-2 [14.2 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main i386 m4 i386 1.4.18-2 [202 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main i386 autoconf all 2.69-11 [322 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main i386 autotools-dev all 20180224.1 [39.6 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main i386 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main i386 autopoint all 0.19.8.1-9 [412 kB] Get:48 http://ftpmaster.internal/ubuntu disco/universe i386 cython i386 0.29.2-2build1 [1235 kB] Get:49 http://ftpmaster.internal/ubuntu disco/universe i386 cython3 i386 0.29.2-2build1 [1258 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main i386 libtool all 2.4.6-9 [194 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main i386 dh-autoreconf all 19 [16.1 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main i386 libarchive-zip-perl all 1.64-1 [84.9 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main i386 libfile-stripnondeterminism-perl all 1.1.0-1 [13.6 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main i386 dh-strip-nondeterminism all 1.1.0-1 [5100 B] Get:55 http://ftpmaster.internal/ubuntu disco/main i386 dwz i386 0.12-3 [81.5 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main i386 libcroco3 i386 0.6.12-3 [87.9 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main i386 gettext i386 0.19.8.1-9 [905 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main i386 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main i386 po-debconf all 1.0.21 [233 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main i386 debhelper all 12ubuntu1 [887 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main i386 python3-lib2to3 all 3.7.2-3ubuntu1 [75.5 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main i386 python3-distutils all 3.7.2-3ubuntu1 [140 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main i386 dh-python all 3.20180927ubuntu2 [90.9 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main i386 libroken18-heimdal i386 7.5.0+dfsg-2.1 [44.7 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main i386 libasn1-8-heimdal i386 7.5.0+dfsg-2.1 [186 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main i386 libblas3 i386 3.8.0-2 [132 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main i386 libbz2-dev i386 1.0.6-9 [31.2 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main i386 libheimbase1-heimdal i386 7.5.0+dfsg-2.1 [32.2 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main i386 libhcrypto4-heimdal i386 7.5.0+dfsg-2.1 [93.4 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main i386 libwind0-heimdal i386 7.5.0+dfsg-2.1 [48.4 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main i386 libhx509-5-heimdal i386 7.5.0+dfsg-2.1 [117 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main i386 libkrb5-26-heimdal i386 7.5.0+dfsg-2.1 [230 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main i386 libheimntlm0-heimdal i386 7.5.0+dfsg-2.1 [16.3 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main i386 libgssapi3-heimdal i386 7.5.0+dfsg-2.1 [106 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main i386 libsasl2-modules-db i386 2.1.27+dfsg-1 [15.8 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main i386 libsasl2-2 i386 2.1.27+dfsg-1 [52.8 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main i386 libldap-common all 2.4.47+dfsg-3ubuntu1 [16.5 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main i386 libldap-2.4-2 i386 2.4.47+dfsg-3ubuntu1 [166 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main i386 libnghttp2-14 i386 1.36.0-2 [84.3 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2 [58.3 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main i386 libssh-4 i386 0.8.6-3 [203 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main i386 libcurl3-gnutls i386 7.63.0-1ubuntu1 [255 kB] Get:83 http://ftpmaster.internal/ubuntu disco/main i386 libcurl4-gnutls-dev i386 7.63.0-1ubuntu1 [350 kB] Get:84 http://ftpmaster.internal/ubuntu disco/universe i386 libdeflate0 i386 1.2-1 [49.9 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main i386 libexpat1-dev i386 2.2.6-1 [137 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main i386 libgfortran5 i386 9-20190207-0ubuntu1 [600 kB] Get:87 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 libhts2 i386 1.9-10 [318 kB] Get:88 http://ftpmaster.internal/ubuntu disco/main i386 liblzma-dev i386 5.2.4-1 [155 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1ubuntu2 [175 kB] Get:90 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 libhts-dev i386 1.9-10 [4281 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main i386 liblapack3 i386 3.8.0-2 [1960 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main i386 libpython2.7 i386 2.7.15-8 [1058 kB] Get:93 http://ftpmaster.internal/ubuntu disco/main i386 libpython2.7-dev i386 2.7.15-8 [31.3 MB] Get:94 http://ftpmaster.internal/ubuntu disco/main i386 libpython2-dev i386 2.7.15-4 [7656 B] Get:95 http://ftpmaster.internal/ubuntu disco/main i386 libpython-dev i386 2.7.15-4 [5892 B] Get:96 http://ftpmaster.internal/ubuntu disco/main i386 libpython-all-dev i386 2.7.15-4 [1104 B] Get:97 http://ftpmaster.internal/ubuntu disco/main i386 libpython3.7 i386 3.7.2-2 [1506 kB] Get:98 http://ftpmaster.internal/ubuntu disco/main i386 libpython3.7-dev i386 3.7.2-2 [47.7 MB] Get:99 http://ftpmaster.internal/ubuntu disco/main i386 libpython3-dev i386 3.7.2-1 [7144 B] Get:100 http://ftpmaster.internal/ubuntu disco/main i386 libpython3-all-dev i386 3.7.2-1 [1108 B] Get:101 http://ftpmaster.internal/ubuntu disco/main i386 libssl-dev i386 1.1.1a-1ubuntu2 [1596 kB] Get:102 http://ftpmaster.internal/ubuntu disco/main i386 python-all i386 2.7.15-4 [1084 B] Get:103 http://ftpmaster.internal/ubuntu disco/main i386 python2.7-dev i386 2.7.15-8 [278 kB] Get:104 http://ftpmaster.internal/ubuntu disco/main i386 python2-dev i386 2.7.15-4 [1252 B] Get:105 http://ftpmaster.internal/ubuntu disco/main i386 python-dev i386 2.7.15-4 [1224 B] Get:106 http://ftpmaster.internal/ubuntu disco/main i386 python-all-dev i386 2.7.15-4 [1112 B] Get:107 http://ftpmaster.internal/ubuntu disco/main i386 python-colorama all 0.3.7-1 [22.6 kB] Get:108 http://ftpmaster.internal/ubuntu disco/main i386 python-click all 7.0-1 [64.6 kB] Get:109 http://ftpmaster.internal/ubuntu disco/main i386 python-monotonic all 1.5-0ubuntu1 [5508 B] Get:110 http://ftpmaster.internal/ubuntu disco/universe i386 python-humanfriendly all 4.17-1 [60.4 kB] Get:111 http://ftpmaster.internal/ubuntu disco/universe i386 python-coloredlogs all 7.3-1 [27.7 kB] Get:112 http://ftpmaster.internal/ubuntu disco-proposed/main i386 python-pkg-resources all 40.8.0-1 [129 kB] Get:113 http://ftpmaster.internal/ubuntu disco/universe i386 python-nose all 1.3.7-4 [116 kB] Get:114 http://ftpmaster.internal/ubuntu disco-proposed/main i386 python-numpy i386 1:1.16.0-1ubuntu1 [2073 kB] Get:115 http://ftpmaster.internal/ubuntu disco-proposed/main i386 python-setuptools all 40.8.0-1 [329 kB] Get:116 http://ftpmaster.internal/ubuntu disco/main i386 python3-all i386 3.7.2-1 [1104 B] Get:117 http://ftpmaster.internal/ubuntu disco/main i386 python3.7-dev i386 3.7.2-2 [511 kB] Get:118 http://ftpmaster.internal/ubuntu disco/main i386 python3-dev i386 3.7.2-1 [1300 B] Get:119 http://ftpmaster.internal/ubuntu disco/main i386 python3-all-dev i386 3.7.2-1 [1104 B] Get:120 http://ftpmaster.internal/ubuntu disco/main i386 python3-colorama all 0.3.7-1 [14.9 kB] Get:121 http://ftpmaster.internal/ubuntu disco/main i386 python3-click all 7.0-1 [64.7 kB] Get:122 http://ftpmaster.internal/ubuntu disco/universe i386 python3-humanfriendly all 4.17-1 [60.5 kB] Get:123 http://ftpmaster.internal/ubuntu disco/universe i386 python3-coloredlogs all 7.3-1 [27.8 kB] Get:124 http://ftpmaster.internal/ubuntu disco-proposed/main i386 python3-pkg-resources all 40.8.0-1 [100 kB] Get:125 http://ftpmaster.internal/ubuntu disco/universe i386 python3-nose all 1.3.7-4 [116 kB] Get:126 http://ftpmaster.internal/ubuntu disco-proposed/main i386 python3-numpy i386 1:1.16.0-1ubuntu1 [2090 kB] Get:127 http://ftpmaster.internal/ubuntu disco-proposed/main i386 python3-setuptools all 40.8.0-1 [252 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 129 MB in 6s (21.1 MB/s) Selecting previously unselected package libpython3.7-minimal:i386. 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Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libgfortran5:i386 (9-20190207-0ubuntu1) ... Setting up libpython2.7-stdlib:i386 (2.7.15-8) ... Setting up autopoint (0.19.8.1-9) ... Setting up libmpdec2:i386 (2.4.2-2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.1.0-1) ... Setting up libk5crypto3:i386 (1.17-1) ... Setting up libpython3.7-stdlib:i386 (3.7.2-2) ... Setting up libwind0-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up gettext (0.19.8.1-9) ... Setting up libasn1-8-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up groff-base (1.22.4-2) ... 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Setting up libpython2-stdlib:i386 (2.7.15-4) ... Setting up libkrb5-3:i386 (1.17-1) ... Setting up libpython2.7-dev:i386 (2.7.15-8) ... Setting up libkrb5-26-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up python2.7-dev (2.7.15-8) ... Setting up libheimntlm0-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up libpython3-dev:i386 (3.7.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libpython3-stdlib:i386 (3.7.2-1) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.2-1) ... Setting up python3-colorama (0.3.7-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3.7-dev (3.7.2-2) ... Setting up python3-humanfriendly (4.17-1) ... Setting up python2 (2.7.15-4) ... Setting up libgssapi-krb5-2:i386 (1.17-1) ... Setting up libpython2-dev:i386 (2.7.15-4) ... Setting up libpython-stdlib:i386 (2.7.15-4) ... Setting up libpython3-all-dev:i386 (3.7.2-1) ... Setting up python3-nose (1.3.7-4) ... Setting up python2-dev (2.7.15-4) ... Setting up libssh-4:i386 (0.8.6-3) ... 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Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-142-generic amd64 (i686) Toolchain package versions: binutils_2.32-1ubuntu4 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-20ubuntu1 gcc-8_8.2.0-20ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-20ubuntu1 libstdc++6_9-20190207-0ubuntu1 linux-libc-dev_4.19.0-13.14 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-1 apt_1.8.0~rc3 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.46 bash_5.0-2ubuntu1 binutils_2.32-1ubuntu4 binutils-common_2.32-1ubuntu4 binutils-i686-linux-gnu_2.32-1ubuntu4 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.33.1-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1ubuntu1 cpp_4:8.2.0-2ubuntu2 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lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu1 lsb-base_10.2018112800ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.33.1-0.1ubuntu1 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20181013-2ubuntu1 ncurses-bin_6.1+20181013-2ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1.1ubuntu1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1build2 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu2 python_2.7.15-4 python-all_2.7.15-4 python-all-dev_2.7.15-4 python-click_7.0-1 python-colorama_0.3.7-1 python-coloredlogs_7.3-1 python-dev_2.7.15-4 python-humanfriendly_4.17-1 python-minimal_2.7.15-4 python-monotonic_1.5-0ubuntu1 python-nose_1.3.7-4 python-numpy_1:1.16.0-1ubuntu1 python-pkg-resources_40.8.0-1 python-setuptools_40.8.0-1 python2_2.7.15-4 python2-dev_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-dev_2.7.15-8 python2.7-minimal_2.7.15-8 python3_3.7.2-1 python3-all_3.7.2-1 python3-all-dev_3.7.2-1 python3-click_7.0-1 python3-colorama_0.3.7-1 python3-coloredlogs_7.3-1 python3-dev_3.7.2-1 python3-distutils_3.7.2-3ubuntu1 python3-humanfriendly_4.17-1 python3-lib2to3_3.7.2-3ubuntu1 python3-minimal_3.7.2-1 python3-nose_1.3.7-4 python3-numpy_1:1.16.0-1ubuntu1 python3-pkg-resources_40.8.0-1 python3-setuptools_40.8.0-1 python3.7_3.7.2-2 python3.7-dev_3.7.2-2 python3.7-minimal_3.7.2-2 readline-common_8.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cyvcf2-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-5ubuntu3 systemd-sysv_240-5ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-5 tzdata_2018i-1 ubuntu-keyring_2018.09.18.1 util-linux_2.33.1-0.1ubuntu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Feb 12 21:19:03 2019 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 ./cyvcf2_0.10.8-1.dsc dpkg-source: info: extracting cyvcf2 in cyvcf2-0.10.8 dpkg-source: info: unpacking cyvcf2_0.10.8.orig.tar.gz dpkg-source: info: unpacking cyvcf2_0.10.8-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_htslib_link_dependency.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-16384954 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16384954 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16384954 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package cyvcf2 dpkg-buildpackage: info: source version 0.10.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from cyvcf2-0.10.8/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python2,python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean running clean removing '/<>/.pybuild/cpython2_2.7_cyvcf2/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.7_cyvcf2/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -rf cyvcf2.egg-info cyvcf2/cyvcf2.c __o.vcf find . -name "*.so" -delete make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 creating /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests running egg_info creating cyvcf2.egg-info writing requirements to cyvcf2.egg-info/requires.txt writing cyvcf2.egg-info/PKG-INFO writing top-level names to cyvcf2.egg-info/top_level.txt writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.pxd -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests running build_ext cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/cyvcf2/cyvcf2.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cyvcf2/cyvcf2.pxd:26:16: Declarations should not be declared inline. warning: cyvcf2/cyvcf2.pxd:188:14: 'BCF_HT_FLAG' redeclared warning: cyvcf2/cyvcf2.pxd:279:30: Declarations should not be declared inline. building 'cyvcf2.cyvcf2' extension creating build creating build/temp.linux-i386-2.7 creating build/temp.linux-i386-2.7/cyvcf2 i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cyvcf2/cyvcf2.c -o build/temp.linux-i386-2.7/cyvcf2/cyvcf2.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:614: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:7883:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:7925:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: cyvcf2/cyvcf2.c:8441:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: cyvcf2/cyvcf2.c:8739:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:8792:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: cyvcf2/cyvcf2.c:9001:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); ^~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: cyvcf2/cyvcf2.c:10286:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 408, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2896:61: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_35__dealloc__’: cyvcf2/cyvcf2.c:11943:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] bcf_hdr_destroy(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} void bcf_hdr_destroy(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: cyvcf2/cyvcf2.c:12424:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); ^~~~~~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /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) ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: cyvcf2/cyvcf2.c:12677:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: cyvcf2/cyvcf2.c:12786:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c:12786:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c:12869:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: cyvcf2/cyvcf2.c:25686:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: cyvcf2/cyvcf2.c:35895:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_6; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:38938:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: cyvcf2/cyvcf2.c:39921:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_i->hdr = __pyx_t_4; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: cyvcf2/cyvcf2.c:40575:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40603:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: cyvcf2/cyvcf2.c:40671:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: cyvcf2/cyvcf2.c:40843:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c:40881:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40940:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2168, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); ~~~~~~~~~~~^ At top level: cyvcf2/cyvcf2.c:6567:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cyvcf2/helpers.c -o build/temp.linux-i386-2.7/cyvcf2/helpers.o i686-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-ZsbYhQ/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cyvcf2/cyvcf2.o build/temp.linux-i386-2.7/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lhts -lcrypt -o /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 creating /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests running egg_info writing cyvcf2.egg-info/PKG-INFO writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing requirements to cyvcf2.egg-info/requires.txt writing top-level names to cyvcf2.egg-info/top_level.txt reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pxd -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests running build_ext skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) building 'cyvcf2.cyvcf2' extension creating build/temp.linux-i386-3.7 creating build/temp.linux-i386-3.7/cyvcf2 i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c cyvcf2/cyvcf2.c -o build/temp.linux-i386-3.7/cyvcf2/cyvcf2.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:614: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:7883:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:7925:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: cyvcf2/cyvcf2.c:8441:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: cyvcf2/cyvcf2.c:8739:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:8792:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: cyvcf2/cyvcf2.c:9001:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); ^~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: cyvcf2/cyvcf2.c:10286:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 408, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2896:61: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_35__dealloc__’: cyvcf2/cyvcf2.c:11943:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] bcf_hdr_destroy(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} void bcf_hdr_destroy(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: cyvcf2/cyvcf2.c:12424:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); ^~~~~~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /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) ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: cyvcf2/cyvcf2.c:12677:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: cyvcf2/cyvcf2.c:12786:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c:12786:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c:12869:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: cyvcf2/cyvcf2.c:25686:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: cyvcf2/cyvcf2.c:35895:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_6; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:38938:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: cyvcf2/cyvcf2.c:39921:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_i->hdr = __pyx_t_4; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: cyvcf2/cyvcf2.c:40575:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40603:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: cyvcf2/cyvcf2.c:40671:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: cyvcf2/cyvcf2.c:40843:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c:40881:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40940:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2168, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); ~~~~~~~~~~~^ At top level: cyvcf2/cyvcf2.c:6567:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c cyvcf2/helpers.c -o build/temp.linux-i386-3.7/cyvcf2/helpers.o i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-3.7/cyvcf2/cyvcf2.o build/temp.linux-i386-3.7/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lhts -lcrypt -o /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.cpython-37m-i386-linux-gnu.so dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:217: cd /<>/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose -v cyvcf2.tests.test_cli.test_version ... ok make sure that we are getting the correct gt_types ... ok cyvcf2.tests.test_reader.test_init ... ok cyvcf2.tests.test_reader.test_type ... ok cyvcf2.tests.test_reader.test_format_str ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_missing_samples ... ok cyvcf2.tests.test_reader.test_ibd ... ok cyvcf2.tests.test_reader.test_relatedness ... tested: 44 variants out of 115 ok cyvcf2.tests.test_reader.test_pls ... ok cyvcf2.tests.test_reader.test_gt_alt_freqs ... ok cyvcf2.tests.test_reader.test_str ... ok cyvcf2.tests.test_reader.test_region ... ok cyvcf2.tests.test_reader.test_empty_info ... ok cyvcf2.tests.test_reader.test_phases ... ok cyvcf2.tests.test_reader.test_bad_init ... [E::hts_open_format] Failed to open file XXXXX ok cyvcf2.tests.test_reader.test_samples ... ok cyvcf2.tests.test_reader.test_next ... ok cyvcf2.tests.test_reader.test_variant ... ok cyvcf2.tests.test_reader.test_info_dict ... ok cyvcf2.tests.test_reader.test_attrs ... ok cyvcf2.tests.test_reader.test_empty ... ok cyvcf2.tests.test_reader.test_format_field ... ok cyvcf2.tests.test_reader.test_writer ... ok cyvcf2.tests.test_reader.test_add_info_to_header ... ok cyvcf2.tests.test_reader.test_read_flag ... ok cyvcf2.tests.test_reader.test_add_flag ... ok cyvcf2.tests.test_reader.test_constants ... ok cyvcf2.tests.test_reader.test_add_filter_to_header ... ok cyvcf2.tests.test_reader.test_seqnames ... ok cyvcf2.tests.test_reader.test_var_type ... ok cyvcf2.tests.test_reader.test_header_info ... ok cyvcf2.tests.test_reader.test_snpeff_header ... ok cyvcf2.tests.test_reader.test_gt_types ... ok cyvcf2.tests.test_reader.test_raw_header ... ok cyvcf2.tests.test_reader.test_iterate ... ok cyvcf2.tests.test_reader.test_empty_call ... ok cyvcf2.tests.test_reader.test_haploid ... ok cyvcf2.tests.test_reader.test_diploid ... ok cyvcf2.tests.test_reader.test_format ... ok cyvcf2.tests.test_reader.test_header_stuff ... ok cyvcf2.tests.test_reader.test_bcf ... OK no intervals found for /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf at 1:69260-69438 ok cyvcf2.tests.test_reader.test_issue12 ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok Ensure gt_bases works with more complex base representations. ... ok cyvcf2.tests.test_reader.test_set_format_float ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) ok cyvcf2.tests.test_reader.test_set_format_int_a ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:581: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([5, 1], dtype=np.int)) ok cyvcf2.tests.test_reader.test_set_format_int_b ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:589: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([855, 11], dtype=np.int64)) ok cyvcf2.tests.test_reader.test_set_format_int_c ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:597: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([9998, 99911], dtype=np.int32)) ok test that we can handle multiple (in this case 3) values per sample ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:607: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("P3", exp) ok cyvcf2.tests.test_reader.test_set_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_info_del ... ok cyvcf2.tests.test_reader.test_filter_id ... ok cyvcf2.tests.test_reader.test_access_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_access_genotype ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_alt_homozygous_gt ... ok cyvcf2.tests.test_reader.test_write_missing_contig ... [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_samples ... ok cyvcf2.tests.test_reader.test_hrec ... ok cyvcf2.tests.test_reader.test_issue44 ... ok cyvcf2.tests.test_reader.test_id_field_updates ... ok cyvcf2.tests.test_reader.test_set_pos ... ok cyvcf2.tests.test_reader.test_set_qual ... ok cyvcf2.tests.test_reader.test_strict_gt_option_flag ... ok cyvcf2.tests.test_reader.test_alt_repr ... ok cyvcf2.tests.test_reader.test_seqlens ... ok cyvcf2.tests.test_reader.test_closed_iter ... ok cyvcf2.tests.test_reader.test_issue72 ... ok cyvcf2.tests.test_reader.test_is_transition ... ok cyvcf2.tests.test_reader.test_decomposed ... ok cyvcf2.tests.test_reader.test_fd ... ok cyvcf2.tests.test_reader.test_set_reference ... ok cyvcf2.tests.test_reader.test_set_alternates ... ok ---------------------------------------------------------------------- Ran 71 tests in 1.661s OK I: pybuild base:217: cd /<>/.pybuild/cpython3_3.7_cyvcf2/build; python3.7 -m nose -v cyvcf2.tests.test_cli.test_version ... ok make sure that we are getting the correct gt_types ... ok cyvcf2.tests.test_reader.test_init ... ok cyvcf2.tests.test_reader.test_type ... ok cyvcf2.tests.test_reader.test_format_str ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_missing_samples ... ok cyvcf2.tests.test_reader.test_ibd ... ok cyvcf2.tests.test_reader.test_relatedness ... tested: 44 variants out of 115 ok cyvcf2.tests.test_reader.test_pls ... ok cyvcf2.tests.test_reader.test_gt_alt_freqs ... ok cyvcf2.tests.test_reader.test_str ... ok cyvcf2.tests.test_reader.test_region ... ok cyvcf2.tests.test_reader.test_empty_info ... ok cyvcf2.tests.test_reader.test_phases ... ok cyvcf2.tests.test_reader.test_bad_init ... [E::hts_open_format] Failed to open file XXXXX ok cyvcf2.tests.test_reader.test_samples ... ok cyvcf2.tests.test_reader.test_next ... ok cyvcf2.tests.test_reader.test_variant ... ok cyvcf2.tests.test_reader.test_info_dict ... ok cyvcf2.tests.test_reader.test_attrs ... ok cyvcf2.tests.test_reader.test_empty ... ok cyvcf2.tests.test_reader.test_format_field ... ok cyvcf2.tests.test_reader.test_writer ... ok cyvcf2.tests.test_reader.test_add_info_to_header ... ok cyvcf2.tests.test_reader.test_read_flag ... ok cyvcf2.tests.test_reader.test_add_flag ... ok cyvcf2.tests.test_reader.test_constants ... ok cyvcf2.tests.test_reader.test_add_filter_to_header ... ok cyvcf2.tests.test_reader.test_seqnames ... ok cyvcf2.tests.test_reader.test_var_type ... ok cyvcf2.tests.test_reader.test_header_info ... ok cyvcf2.tests.test_reader.test_snpeff_header ... ok cyvcf2.tests.test_reader.test_gt_types ... ok cyvcf2.tests.test_reader.test_raw_header ... ok cyvcf2.tests.test_reader.test_iterate ... ok cyvcf2.tests.test_reader.test_empty_call ... ok cyvcf2.tests.test_reader.test_haploid ... ok cyvcf2.tests.test_reader.test_diploid ... ok cyvcf2.tests.test_reader.test_format ... ok cyvcf2.tests.test_reader.test_header_stuff ... ok cyvcf2.tests.test_reader.test_bcf ... OK no intervals found for b'/<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf' at 1:69260-69438 ok cyvcf2.tests.test_reader.test_issue12 ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok Ensure gt_bases works with more complex base representations. ... ok cyvcf2.tests.test_reader.test_set_format_float ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) ok cyvcf2.tests.test_reader.test_set_format_int_a ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:581: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([5, 1], dtype=np.int)) ok cyvcf2.tests.test_reader.test_set_format_int_b ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:589: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([855, 11], dtype=np.int64)) ok cyvcf2.tests.test_reader.test_set_format_int_c ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:597: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([9998, 99911], dtype=np.int32)) ok test that we can handle multiple (in this case 3) values per sample ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:607: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("P3", exp) ok cyvcf2.tests.test_reader.test_set_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_info_del ... ok cyvcf2.tests.test_reader.test_filter_id ... ok cyvcf2.tests.test_reader.test_access_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_access_genotype ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_alt_homozygous_gt ... ok cyvcf2.tests.test_reader.test_write_missing_contig ... [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_samples ... ok cyvcf2.tests.test_reader.test_hrec ... ok cyvcf2.tests.test_reader.test_issue44 ... ok cyvcf2.tests.test_reader.test_id_field_updates ... ok cyvcf2.tests.test_reader.test_set_pos ... ok cyvcf2.tests.test_reader.test_set_qual ... ok cyvcf2.tests.test_reader.test_strict_gt_option_flag ... ok cyvcf2.tests.test_reader.test_alt_repr ... ok cyvcf2.tests.test_reader.test_seqlens ... ok cyvcf2.tests.test_reader.test_closed_iter ... ok cyvcf2.tests.test_reader.test_issue72 ... ok cyvcf2.tests.test_reader.test_is_transition ... ok cyvcf2.tests.test_reader.test_decomposed ... ok cyvcf2.tests.test_reader.test_fd ... ok cyvcf2.tests.test_reader.test_set_reference ... ok cyvcf2.tests.test_reader.test_set_alternates ... ok ---------------------------------------------------------------------- Ran 71 tests in 1.311s OK create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python2,python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install I: pybuild base:217: /usr/bin/python setup.py install --root /<>/debian/python-cyvcf2 running install running build running build_py running egg_info writing requirements to cyvcf2.egg-info/requires.txt writing cyvcf2.egg-info/PKG-INFO writing top-level names to cyvcf2.egg-info/top_level.txt writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 running build_ext skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) running install_lib creating /<>/debian/python-cyvcf2 creating /<>/debian/python-cyvcf2/usr creating /<>/debian/python-cyvcf2/usr/lib creating /<>/debian/python-cyvcf2/usr/lib/python2.7 creating /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages creating /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.pyx -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.pxd -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__init__.pyc -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__init__.py -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cli.pyc -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__main__.py -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/relatedness.h -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.c -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cli.py -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/helpers.h -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 creating /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_cli.pyc -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/__init__.pyc -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/issue_44.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_hemi.py -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf.csi -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_hemi.pyc -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/__init__.py -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/o.vcf.gz -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-hemi.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz.tbi -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_cli.py -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/decomposed.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/empty.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-format-string.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.comp_het.3.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/seg.vcf.gz -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-alt-repr.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/bug.vcf.gz -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.pyc -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-haploidX.vcf -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/helpers.c -> /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 byte-compiling /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/__init__.py to __init__.pyc byte-compiling /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/__main__.py to __main__.pyc byte-compiling /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cli.py to cli.pyc byte-compiling /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/test_hemi.py to test_hemi.pyc byte-compiling /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/__init__.py to __init__.pyc byte-compiling /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/test_cli.py to test_cli.pyc byte-compiling /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/test_reader.py to test_reader.pyc running install_egg_info Copying cyvcf2.egg-info to /<>/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info Skipping SOURCES.txt running install_scripts Installing cyvcf2 script to /<>/debian/python-cyvcf2/usr/bin I: pybuild base:217: /usr/bin/python3 setup.py install --root /<>/debian/python3-cyvcf2 running install running build running build_py running egg_info writing cyvcf2.egg-info/PKG-INFO writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing requirements to cyvcf2.egg-info/requires.txt writing top-level names to cyvcf2.egg-info/top_level.txt reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' running build_ext skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) running install_lib creating /<>/debian/python3-cyvcf2 creating /<>/debian/python3-cyvcf2/usr creating /<>/debian/python3-cyvcf2/usr/lib creating /<>/debian/python3-cyvcf2/usr/lib/python3.7 creating /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages creating /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.pyx -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.pxd -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.cpython-37m-i386-linux-gnu.so -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__init__.py -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__main__.py -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/relatedness.h -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.c -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 creating /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__pycache__/__init__.cpython-37.pyc -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__pycache__/cli.cpython-37.pyc -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cli.py -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/helpers.h -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 creating /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/issue_44.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_hemi.py -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf.csi -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__init__.py -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/o.vcf.gz -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-hemi.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz.tbi -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests creating /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/__init__.cpython-37.pyc -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/test_cli.cpython-37.pyc -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/test_hemi.cpython-37.pyc -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/test_reader.cpython-37.pyc -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_cli.py -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/decomposed.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/empty.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-format-string.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.comp_het.3.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/seg.vcf.gz -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-alt-repr.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/bug.vcf.gz -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-haploidX.vcf -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/helpers.c -> /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 byte-compiling /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__main__.py to __main__.cpython-37.pyc byte-compiling /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/cli.py to cli.cpython-37.pyc byte-compiling /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/test_hemi.py to test_hemi.cpython-37.pyc byte-compiling /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/test_cli.py to test_cli.cpython-37.pyc byte-compiling /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/test_reader.py to test_reader.cpython-37.pyc running install_egg_info Copying cyvcf2.egg-info to /<>/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2-0.10.8.egg-info Skipping SOURCES.txt running install_scripts Installing cyvcf2 script to /<>/debian/python3-cyvcf2/usr/bin rm -f debian/python-cyvcf2/usr/bin/cyvcf2 make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_numpy dh_install make[1]: Leaving directory '/<>' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python2 -a -O--buildsystem=pybuild I: dh_python2 fs:329: renaming cyvcf2.so to cyvcf2.i386-linux-gnu.so dh_python3 -a -O--buildsystem=pybuild dh_installinit -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing python3-cyvcf2 (in debian/python3-cyvcf2); do_strip: , oemstrip: pkgstriptranslations: processing python3-cyvcf2-dbgsym (in debian/.debhelper/python3-cyvcf2/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python-cyvcf2 (in debian/python-cyvcf2); do_strip: , oemstrip: pkgstriptranslations: processing python-cyvcf2-dbgsym (in debian/.debhelper/python-cyvcf2/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-cyvcf2/DEBIAN/control, package python3-cyvcf2, directory debian/python3-cyvcf2 INFO: pkgstripfiles: waiting for lock (python3-cyvcf2) ... pkgstripfiles: processing control file: debian/python-cyvcf2/DEBIAN/control, package python-cyvcf2, directory debian/python-cyvcf2 pkgstripfiles: processing control file: debian/.debhelper/python-cyvcf2/dbgsym-root/DEBIAN/control, package python-cyvcf2-dbgsym, directory debian/.debhelper/python-cyvcf2/dbgsym-root dpkg-deb: building package 'python-cyvcf2-dbgsym' in 'debian/.debhelper/scratch-space/build-python-cyvcf2/python-cyvcf2-dbgsym_0.10.8-1_i386.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-cyvcf2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-cyvcf2' in '../python-cyvcf2_0.10.8-1_i386.deb'. Renaming python-cyvcf2-dbgsym_0.10.8-1_i386.deb to python-cyvcf2-dbgsym_0.10.8-1_i386.ddeb pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-cyvcf2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-cyvcf2' in '../python3-cyvcf2_0.10.8-1_i386.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python3-cyvcf2/dbgsym-root/DEBIAN/control, package python3-cyvcf2-dbgsym, directory debian/.debhelper/python3-cyvcf2/dbgsym-root dpkg-deb: building package 'python3-cyvcf2-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-cyvcf2/python3-cyvcf2-dbgsym_0.10.8-1_i386.deb'. Renaming python3-cyvcf2-dbgsym_0.10.8-1_i386.deb to python3-cyvcf2-dbgsym_0.10.8-1_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../cyvcf2_0.10.8-1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from cyvcf2-0.10.8/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20190213-0511 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ cyvcf2_0.10.8-1_i386.changes: ----------------------------- Format: 1.8 Date: Tue, 12 Feb 2019 22:12:40 +0100 Source: cyvcf2 Binary: python-cyvcf2 python3-cyvcf2 Architecture: i386 Version: 0.10.8-1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: python-cyvcf2 - VCF parser based on htslib (Python 2) python3-cyvcf2 - VCF parser based on htslib (Python 3) Changes: cyvcf2 (0.10.8-1) unstable; urgency=medium . * Team upload. * New upstream version Checksums-Sha1: 26b3ec8d1792e29f73ff41722dbe07f9318dc799 8794 cyvcf2_0.10.8-1_i386.buildinfo 4d8ff5bd94e35e47421559cac1bf12a79104c15d 739512 python-cyvcf2-dbgsym_0.10.8-1_i386.ddeb c201cb7ba5aeffc71e1465c1579afcf05f0a8024 764756 python-cyvcf2_0.10.8-1_i386.deb 7a953fac887d38a6e5902904b48989f12e20b12c 897548 python3-cyvcf2-dbgsym_0.10.8-1_i386.ddeb 65172b91def528901937be3fb096d015489b9b33 769984 python3-cyvcf2_0.10.8-1_i386.deb Checksums-Sha256: 1fa193ba2fc3b87c17b54da825ab3def2e0219795151dd3f63861bfeda0c2249 8794 cyvcf2_0.10.8-1_i386.buildinfo ee9c09a5cf852c2ae480fb10d8702d47388e79512fdba06a70d136b2f85f8d67 739512 python-cyvcf2-dbgsym_0.10.8-1_i386.ddeb 05a6ad1e3283c2fa81d77205479091c824b87767fb81f62021cebdb61d147b43 764756 python-cyvcf2_0.10.8-1_i386.deb 5a1cbe4dddb6dea21f55d160c9e22d260807268c11d33540d08e71569afed176 897548 python3-cyvcf2-dbgsym_0.10.8-1_i386.ddeb 772d7e839d1203fd4da1ab00e6bf163310ed82a5eb8f53c3ae5276a5a256b133 769984 python3-cyvcf2_0.10.8-1_i386.deb Files: 10249c6b6cd68f59d89a20ae46784560 8794 science optional cyvcf2_0.10.8-1_i386.buildinfo 2069f8e6e54ba62038829bd1b937541d 739512 debug optional python-cyvcf2-dbgsym_0.10.8-1_i386.ddeb 32570278b102ebcd66e01991c5764c27 764756 python optional python-cyvcf2_0.10.8-1_i386.deb 3aa0fc0b6928a36af567cde40aa92b5f 897548 debug optional python3-cyvcf2-dbgsym_0.10.8-1_i386.ddeb 8ba630f4c88796e1a2d3da730000eadb 769984 python optional python3-cyvcf2_0.10.8-1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-cyvcf2_0.10.8-1_i386.deb ------------------------------- new debian package, version 2.0. size 764756 bytes: control archive=2356 bytes. 1011 bytes, 22 lines control 4249 bytes, 45 lines md5sums 163 bytes, 9 lines * postinst #!/bin/sh 265 bytes, 14 lines * prerm #!/bin/sh Package: python-cyvcf2 Source: cyvcf2 Version: 0.10.8-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4515 Depends: python-numpy (>= 1:1.16.0~rc1), python-numpy-abi9, python (<< 2.8), python (>= 2.7~), python:any (<< 2.8), python:any (>= 2.7~), libc6 (>= 2.7), libhts2 (>= 1.2.1) Suggests: python-cyvcf2-doc Section: python Priority: optional Homepage: https://github.com/brentp/cyvcf2 Description: VCF parser based on htslib (Python 2) This modules allows fast parsing of VCF and BCF including region-queries with Python. This is essential for efficient analyses of nucleotide variation with Python on high-throughput sequencing data. . cyvcf2 is a cython wrapper around htslib. Attributes like variant.gt_ref_depths return a numpy array directly so they are immediately ready for downstream use. . This package installs the library for Python 2. drwxr-xr-x root/root 0 2019-02-12 21:12 ./ drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/ drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/lib/ drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info/ -rw-r--r-- root/root 5699 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info/PKG-INFO -rw-r--r-- root/root 1 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info/dependency_links.txt -rw-r--r-- root/root 48 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info/entry_points.txt -rw-r--r-- root/root 1 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info/not-zip-safe -rw-r--r-- root/root 0 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info/requires.txt -rw-r--r-- root/root 7 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2-0.10.8.egg-info/top_level.txt drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/ -rw-r--r-- root/root 157 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/__init__.py -rw-r--r-- root/root 326 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/__main__.py -rw-r--r-- root/root 5114 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/cli.py -rw-r--r-- root/root 2778922 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.c -rw-r--r-- root/root 738096 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.i386-linux-gnu.so -rw-r--r-- root/root 12386 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.pxd -rw-r--r-- root/root 77015 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.pyx -rw-r--r-- root/root 3448 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/helpers.c -rw-r--r-- root/root 248 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/helpers.h -rw-r--r-- root/root 6288 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/relatedness.h drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/ -rw-r--r-- root/root 2 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/__init__.py -rw-r--r-- root/root 5389 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/bug.vcf.gz -rw-r--r-- root/root 456 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/decomposed.vcf -rw-r--r-- root/root 0 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/empty.vcf -rw-r--r-- root/root 588 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/issue_44.vcf -rw-r--r-- root/root 48729 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/o.vcf.gz -rw-r--r-- root/root 878 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/seg.vcf.gz -rw-r--r-- root/root 2555 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-alt-repr.vcf -rw-r--r-- root/root 881 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-format-string.vcf -rw-r--r-- root/root 597572 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-haploidX.vcf -rw-r--r-- root/root 20052 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-hemi.vcf -rw-r--r-- root/root 327 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -rw-r--r-- root/root 104 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -rw-r--r-- root/root 368 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -rw-r--r-- root/root 103 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -rw-r--r-- root/root 19144 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test.comp_het.3.vcf -rw-r--r-- root/root 5121 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test.snpeff.bcf -rw-r--r-- root/root 117 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test.snpeff.bcf.csi -rw-r--r-- root/root 17254 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test.snpeff.vcf -rw-r--r-- root/root 174816 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test.vcf.gz -rw-r--r-- root/root 103 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test.vcf.gz.tbi -rw-r--r-- root/root 334 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test_cli.py -rw-r--r-- root/root 21089 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test_gt_alt_freqs.vcf -rw-r--r-- root/root 6188 2019-02-12 21:12 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test_gt_bases.vcf.gz -rw-r--r-- root/root 767 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test_hemi.py -rw-r--r-- root/root 29206 2019-02-07 17:58 ./usr/lib/python2.7/dist-packages/cyvcf2/tests/test_reader.py drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/share/ drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-02-12 21:12 ./usr/share/doc/python-cyvcf2/ -rw-r--r-- root/root 197 2019-02-12 21:12 ./usr/share/doc/python-cyvcf2/README.Debian -rw-r--r-- root/root 914 2019-02-12 21:12 ./usr/share/doc/python-cyvcf2/changelog.Debian.gz -rw-r--r-- root/root 1331 2019-02-12 21:12 ./usr/share/doc/python-cyvcf2/copyright python3-cyvcf2_0.10.8-1_i386.deb -------------------------------- new debian package, version 2.0. size 769984 bytes: control archive=2440 bytes. 948 bytes, 22 lines control 4152 bytes, 45 lines md5sums 254 bytes, 12 lines * postinst #!/bin/sh 403 bytes, 12 lines * prerm #!/bin/sh Package: python3-cyvcf2 Source: cyvcf2 Version: 0.10.8-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4528 Depends: python3 (<< 3.8), python3 (>= 3.7~), python3-numpy, python3:any, libc6 (>= 2.7), libhts2 (>= 1.2.1) Suggests: python-cyvcf2-doc Section: python Priority: optional Homepage: https://github.com/brentp/cyvcf2 Description: VCF parser based on htslib (Python 3) This modules allows fast parsing of VCF and BCF including region-queries with Python. This is essential for efficient analyses of nucleotide variation with Python on high-throughput sequencing data. . cyvcf2 is a cython wrapper around htslib. Attributes like variant.gt_ref_depths return a numpy array directly so they are immediately ready for downstream use. . 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 41460 Build-Time: 87 Distribution: disco-proposed Host Architecture: i386 Install-Time: 43 Job: cyvcf2_0.10.8-1.dsc Machine Architecture: amd64 Package: cyvcf2 Package-Time: 131 Source-Version: 0.10.8-1 Space: 41460 Status: successful Version: 0.10.8-1 -------------------------------------------------------------------------------- Finished at 20190213-0511 Build needed 00:02:11, 41460k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16384954 Scanning for processes to kill in build PACKAGEBUILD-16384954