RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos01-ppc64el-009 4.4.0-98-generic #121-Ubuntu SMP Tue Oct 10 14:23:01 UTC 2017 ppc64le Buildd toolchain package versions: launchpad-buildd_154 python-lpbuildd_154 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_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 10 Nov 23:31:44 ntpdate[1786]: adjust time server 10.211.37.1 offset 0.079612 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13709260 /home/buildd/filecache-default/64ab4a3b1843816d631a3747c16f42fa2d8de59d Creating target for build PACKAGEBUILD-13709260 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13709260 Starting target for build PACKAGEBUILD-13709260 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13709260 'deb http://ftpmaster.internal/ubuntu bionic main universe' 'deb http://ftpmaster.internal/ubuntu bionic-security main universe' 'deb http://ftpmaster.internal/ubuntu bionic-updates main universe' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-13709260 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13709260 Updating target for build PACKAGEBUILD-13709260 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main ppc64el Packages [1015 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [541 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe ppc64el Packages [7977 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4860 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el Packages [180 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [96.6 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el Packages [790 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [449 kB] Fetched 16.4 MB in 3s (4769 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: liblsan0 libtsan0 The following packages will be upgraded: apt apt-transport-https base-files base-passwd binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils build-essential coreutils cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcomerr2 libcurl3-gnutls libdpkg-perl libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libhogweed4 libitm1 libkeyutils1 libmount1 libnettle6 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libubsan0 libudev1 libuuid1 linux-libc-dev mount multiarch-support openssl perl perl-base perl-modules-5.26 pinentry-curses systemd systemd-sysv sysvinit-utils tzdata util-linux 85 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 58.4 MB of archives. After this operation, 8850 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main ppc64el base-files ppc64el 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el bsdutils ppc64el 1:2.30.1-0ubuntu5 [61.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main ppc64el coreutils ppc64el 8.26-3ubuntu4 [1251 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el debianutils ppc64el 4.8.3 [86.0 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg ppc64el 1.19.0.4ubuntu1 [1149 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6-dev ppc64el 2.26-0ubuntu2 [2458 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-dev-bin ppc64el 2.26-0ubuntu2 [65.4 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main ppc64el linux-libc-dev ppc64el 4.13.0-16.19 [946 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libitm1 ppc64el 7.2.0-13ubuntu1 [29.7 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el gcc-7-base ppc64el 7.2.0-13ubuntu1 [18.5 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgcc1 ppc64el 1:7.2.0-13ubuntu1 [29.8 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgomp1 ppc64el 7.2.0-13ubuntu1 [69.3 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libatomic1 ppc64el 7.2.0-13ubuntu1 [8552 B] Get:14 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libasan4 ppc64el 7.2.0-13ubuntu1 [367 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el liblsan0 ppc64el 7.2.0-13ubuntu1 [134 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libtsan0 ppc64el 7.2.0-13ubuntu1 [287 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libubsan0 ppc64el 7.2.0-13ubuntu1 [136 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el cpp-7 ppc64el 7.2.0-13ubuntu1 [6261 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libcc1-0 ppc64el 7.2.0-13ubuntu1 [39.3 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el g++-7 ppc64el 7.2.0-13ubuntu1 [7102 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el gcc-7 ppc64el 7.2.0-13ubuntu1 [6899 kB] Get:22 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgcc-7-dev ppc64el 7.2.0-13ubuntu1 [983 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libstdc++-7-dev ppc64el 7.2.0-13ubuntu1 [1524 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libstdc++6 ppc64el 7.2.0-13ubuntu1 [441 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgmp10 ppc64el 2:6.1.2+dfsg-1.1 [218 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libbinutils ppc64el 2.29.1-7ubuntu1 [457 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el binutils ppc64el 2.29.1-7ubuntu1 [3408 B] Get:28 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el binutils-common ppc64el 2.29.1-7ubuntu1 [190 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.29.1-7ubuntu1 [1968 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6 ppc64el 2.26-0ubuntu2 [2619 kB] Get:31 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el e2fslibs ppc64el 1.43.7-1 [173 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el e2fsprogs ppc64el 1.43.7-1 [510 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el findutils ppc64el 4.6.0+git+20170828-2 [314 kB] Get:34 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el perl-modules-5.26 all 5.26.1-2ubuntu1 [2760 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libperl5.26 ppc64el 5.26.1-2ubuntu1 [3405 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el perl ppc64el 5.26.1-2ubuntu1 [201 kB] Get:37 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el perl-base ppc64el 5.26.1-2ubuntu1 [1303 kB] Get:38 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libuuid1 ppc64el 2.30.1-0ubuntu5 [15.3 kB] Get:39 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libblkid1 ppc64el 2.30.1-0ubuntu5 [128 kB] Get:40 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libfdisk1 ppc64el 2.30.1-0ubuntu5 [160 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpcre3 ppc64el 2:8.39-5ubuntu3 [224 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libselinux1 ppc64el 2.7-2 [78.6 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libmount1 ppc64el 2.30.1-0ubuntu5 [139 kB] Get:44 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libsmartcols1 ppc64el 2.30.1-0ubuntu5 [84.6 kB] Get:45 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el fdisk ppc64el 2.30.1-0ubuntu5 [108 kB] Get:46 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el util-linux ppc64el 2.30.1-0ubuntu5 [878 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main ppc64el base-passwd ppc64el 3.5.44 [50.1 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-bin ppc64el 2.26-0ubuntu2 [573 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main ppc64el sysvinit-utils ppc64el 2.88dsf-59.10ubuntu1 [20.6 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libudev1 ppc64el 235-2ubuntu2 [60.2 kB] Get:51 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libapt-pkg5.0 ppc64el 1.6~alpha4 [879 kB] Get:52 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgpg-error0 ppc64el 1.27-5 [42.1 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgcrypt20 ppc64el 1.7.9-2 [440 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main ppc64el gpgv ppc64el 2.1.15-1ubuntu8 [218 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main ppc64el libseccomp2 ppc64el 2.3.1-2.1ubuntu3 [47.2 kB] Get:56 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el apt ppc64el 1.6~alpha4 [1191 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el debconf all 1.5.64 [124 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libapparmor1 ppc64el 2.11.0-2ubuntu18 [29.9 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap2 ppc64el 1:2.25-1.1 [13.7 kB] Get:60 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el mount ppc64el 2.30.1-0ubuntu5 [111 kB] Get:61 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el systemd ppc64el 235-2ubuntu2 [2959 kB] Get:62 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libsystemd0 ppc64el 235-2ubuntu2 [213 kB] Get:63 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el systemd-sysv ppc64el 235-2ubuntu2 [12.4 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap-ng0 ppc64el 0.7.7-3.1 [11.6 kB] Get:65 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libcomerr2 ppc64el 1.43.7-1 [11.6 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage-common all 2.7-2 [6916 B] Get:67 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage1 ppc64el 2.7-2 [85.4 kB] Get:68 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libss2 ppc64el 1.43.7-1 [11.4 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnettle6 ppc64el 3.3-2 [120 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhogweed4 ppc64el 3.3-2 [134 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main ppc64el libp11-kit0 ppc64el 0.23.9-2 [167 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main ppc64el pinentry-curses ppc64el 1.0.0-3 [37.5 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg ppc64el 2.1.15-1ubuntu8 [847 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg-agent ppc64el 2.1.15-1ubuntu8 [291 kB] Get:75 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libsqlite3-0 ppc64el 3.21.0-1 [464 kB] Get:76 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libssl1.0.0 ppc64el 1.0.2g-1ubuntu14 [880 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main ppc64el multiarch-support ppc64el 2.26-0ubuntu2 [6832 B] Get:78 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el openssl ppc64el 1.0.2g-1ubuntu14 [520 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main ppc64el tzdata all 2017c-1 [188 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main ppc64el libkeyutils1 ppc64el 1.5.9-9.1ubuntu1 [9896 B] Get:81 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpng16-16 ppc64el 1.6.34-1 [200 kB] Get:82 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el apt-transport-https all 1.6~alpha4 [1692 B] Get:83 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main ppc64el libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main ppc64el build-essential ppc64el 12.4ubuntu1 [4754 B] Get:86 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libpsl5 ppc64el 0.18.0-4 [42.6 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcurl3-gnutls ppc64el 7.55.1-1ubuntu2.1 [197 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.4 MB in 1s (31.2 MB/s) (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../base-files_10ubuntu1_ppc64el.deb ... Unpacking base-files (10ubuntu1) over (9.6ubuntu101) ... Setting up base-files (10ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.30.1-0ubuntu5_ppc64el.deb ... Unpacking bsdutils (1:2.30.1-0ubuntu5) over (1:2.30.1-0ubuntu4) ... Setting up bsdutils (1:2.30.1-0ubuntu5) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../coreutils_8.26-3ubuntu4_ppc64el.deb ... Unpacking coreutils (8.26-3ubuntu4) over (8.26-3ubuntu3) ... Setting up coreutils (8.26-3ubuntu4) ... (Reading database ... 12537 files and directories currently installed.) 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Setting up binutils (2.29.1-7ubuntu1) ... Setting up gcc-7 (7.2.0-13ubuntu1) ... Setting up g++-7 (7.2.0-13ubuntu1) ... Setting up libdpkg-perl (1.19.0.4ubuntu1) ... Setting up dpkg-dev (1.19.0.4ubuntu1) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13709260 ppc64el bionic-proposed -c chroot:build-PACKAGEBUILD-13709260 --arch=ppc64el --dist=bionic-proposed --nolog python-pysam_0.12.0.1+ds-4.dsc Initiating build PACKAGEBUILD-13709260 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-98-generic #121-Ubuntu SMP Tue Oct 10 14:23:01 UTC 2017 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-ppc64el-009.buildd +==============================================================================+ | python-pysam 0.12.0.1+ds-4 (ppc64el) 10 Nov 2017 23:32 | +==============================================================================+ Package: python-pysam Version: 0.12.0.1+ds-4 Source Version: 0.12.0.1+ds-4 Distribution: bionic-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/python-pysam-R6Sqis/python-pysam-0.12.0.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-R6Sqis' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13709260/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.12.0.1+ds-4.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-b20zUX/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-b20zUX/apt_archive ./ InRelease Get:2 copy:/<>/resolver-b20zUX/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-b20zUX/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-b20zUX/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-b20zUX/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (254 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 packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use 'apt autoremove' to remove them. 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-b20zUX/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12547 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), dh-exec, dh-python, libhts-dev (>= 1.5-3), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.5), bcftools (>= 1.5), python-pytest, python3-pytest Filtered Build-Depends: debhelper (>= 10), dh-exec, dh-python, libhts-dev (>= 1.5-3), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.5), bcftools (>= 1.5), python-pytest, python3-pytest dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-HoLLBt/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-HoLLBt/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HoLLBt/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-HoLLBt/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HoLLBt/apt_archive ./ Sources [315 B] Get:5 copy:/<>/resolver-HoLLBt/apt_archive ./ Packages [626 B] Fetched 3060 B in 0s (285 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-pysam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu60 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-pkg-resources python-py python-pytest python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-pkg-resources python3-py python3-pytest python3-setuptools python3.6 python3.6-dev python3.6-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk subversion python-pytest-xdist python-mock python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.6-venv python3.6-doc Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl cwltool The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu60 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-pkg-resources python-py python-pytest python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-pkg-resources python3-py python3-pytest python3-setuptools python3.6 python3.6-dev python3.6-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 83 newly installed, 1 to remove and 0 not upgraded. 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Setting up libarchive-zip-perl (1.59-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:ppc64el (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:ppc64el (2.54.1-1ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-4ubuntu1) ... Setting up libpipeline1:ppc64el (1.4.2-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:ppc64el (0.8.6-3) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-5ubuntu2) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:ppc64el (1:5.32-1) ... Setting up libcroco3:ppc64el (0.6.12-1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up autotools-dev (20161112.1+nmu1) ... Setting up libexpat1-dev:ppc64el (2.2.3-2) ... Setting up tabix (1.5-3) ... Setting up liblzma-dev:ppc64el (5.2.2-1.3) ... Setting up bsdmainutils (9.0.12+nmu1ubuntu1) ... 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 libhts2:ppc64el (1.5-3) ... Setting up libpython2.7-stdlib:ppc64el (2.7.14-2ubuntu2) ... Setting up autopoint (0.19.8.1-4ubuntu1) ... Setting up libmpdec2:ppc64el (2.4.2-1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up libpython3.6-stdlib:ppc64el (3.6.3-1ubuntu1) ... Setting up python3.6 (3.6.3-1ubuntu1) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up libhts-dev:ppc64el (1.5-3) ... Setting up python2.7 (2.7.14-2ubuntu2) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up libpython-stdlib:ppc64el (2.7.14-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython2.7:ppc64el (2.7.14-2ubuntu2) ... Setting up automake (1:1.15.1-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2.7-dev:ppc64el (2.7.14-2ubuntu2) ... Setting up samtools (1.5-1build1) ... Setting up bcftools (1.5-3) ... Setting up python2.7-dev (2.7.14-2ubuntu2) ... Setting up python (2.7.14-2ubuntu1) ... Setting up libpython3.6:ppc64el (3.6.3-1ubuntu1) ... Setting up libtool (2.4.6-2) ... Setting up libpython3-stdlib:ppc64el (3.6.3-2) ... Setting up libpython-dev:ppc64el (2.7.14-2ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up python-dev (2.7.14-2ubuntu1) ... Setting up libpython-all-dev:ppc64el (2.7.14-2ubuntu1) ... Setting up python-pkg-resources (36.6.0-1) ... Setting up libpython3.6-dev:ppc64el (3.6.3-1ubuntu1) ... Setting up cython (0.26.1-0.4) ... Setting up python3.6-dev (3.6.3-1ubuntu1) ... Setting up python-all (2.7.14-2ubuntu1) ... Setting up libpython3-dev:ppc64el (3.6.3-2) ... Setting up python-setuptools (36.6.0-1) ... Setting up python-py (1.4.34-3) ... Setting up python-pytest (3.2.1-2) ... Setting up python-all-dev (2.7.14-2ubuntu1) ... Setting up libpython3-all-dev:ppc64el (3.6.3-2) ... Setting up dh-autoreconf (14) ... Setting up python3 (3.6.3-2) ... Setting up python3-dev (3.6.3-2) ... Setting up python3-pkg-resources (36.6.0-1) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up python3-all (3.6.3-2) ... Setting up cython3 (0.26.1-0.4) ... Setting up python3-setuptools (36.6.0-1) ... Setting up dh-python (2.20170125) ... Setting up debhelper (10.10.5ubuntu1) ... Setting up python3-py (1.4.34-3) ... Setting up python3-all-dev (3.6.3-2) ... Setting up python3-pytest (3.2.1-2) ... Setting up dh-exec (0.23build1) ... Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ... (Reading database ... 17793 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-98-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.29.1-7ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-13ubuntu1 gcc-7_7.2.0-13ubuntu1 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-13ubuntu1 libstdc++6_7.2.0-13ubuntu1 linux-libc-dev_4.13.0-16.19 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.6~alpha4 apt-transport-https_1.6~alpha4 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1+nmu1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4-5ubuntu1 bcftools_1.5-3 binutils_2.29.1-7ubuntu1 binutils-common_2.29.1-7ubuntu1 binutils-powerpc64le-linux-gnu_2.29.1-7ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu5 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3ubuntu4 cpp_4:7.2.0-1ubuntu1 cpp-7_7.2.0-13ubuntu1 cython_0.26.1-0.4 cython3_0.26.1-0.4 dash_0.5.8-2.3ubuntu1 debconf_1.5.64 debhelper_10.10.5ubuntu1 debianutils_4.8.3 dh-autoreconf_14 dh-exec_0.23build1 dh-python_2.20170125 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2ubuntu3 dpkg_1.19.0.4ubuntu1 dpkg-dev_1.19.0.4ubuntu1 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 fakeroot_1.21-1ubuntu2 fdisk_2.30.1-0ubuntu5 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1ubuntu1 g++-7_7.2.0-13ubuntu1 gcc_4:7.2.0-1ubuntu1 gcc-7_7.2.0-13ubuntu1 gcc-7-base_7.2.0-13ubuntu1 gettext_0.19.8.1-4ubuntu1 gettext-base_0.19.8.1-4ubuntu1 gnupg_2.1.15-1ubuntu8 gnupg-agent_2.1.15-1ubuntu8 gpgv_2.1.15-1ubuntu8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.49ubuntu1 init-system-helpers_1.49ubuntu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu18 libapt-pkg5.0_1.6~alpha4 libarchive-zip-perl_1.59-1 libasan4_7.2.0-13ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-3 libatomic1_7.2.0-13ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu2 libaudit1_1:2.7.7-1ubuntu2 libbinutils_2.29.1-7ubuntu1 libblkid1_2.30.1-0ubuntu5 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-0ubuntu2 libc-dev-bin_2.26-0ubuntu2 libc6_2.26-0ubuntu2 libc6-dev_2.26-0ubuntu2 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-13ubuntu1 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4ubuntu1 libcurl3-gnutls_7.55.1-1ubuntu2.1 libdb5.3_5.3.28-13.1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu3 libdpkg-perl_1.19.0.4ubuntu1 libexpat1_2.2.3-2 libexpat1-dev_2.2.3-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.30.1-0ubuntu5 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-13ubuntu1 libgcc1_1:7.2.0-13ubuntu1 libgcrypt20_1.7.9-2 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1ubuntu1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.8-6ubuntu3 libgomp1_7.2.0-13ubuntu1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.15.1-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 libhcrypto4-heimdal_7.4.0.dfsg.1-2 libheimbase1-heimdal_7.4.0.dfsg.1-2 libheimntlm0-heimdal_7.4.0.dfsg.1-2 libhogweed4_3.3-2 libhts-dev_1.5-3 libhts2_1.5-3 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu60_60.1-1ubuntu2 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libitm1_7.2.0-13ubuntu1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9.1ubuntu1 libkmod2_24-1ubuntu2 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblsan0_7.2.0-13ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.1-0ubuntu5 libmpc3_1.0.3-2 libmpdec2_2.4.2-1 libmpfr4_3.1.6-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-2 libnpth0_1.5-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-5ubuntu3 libperl5.26_5.26.1-2ubuntu1 libpipeline1_1.4.2-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.18.0-4 libpython-all-dev_2.7.14-2ubuntu1 libpython-dev_2.7.14-2ubuntu1 libpython-stdlib_2.7.14-2ubuntu1 libpython2.7_2.7.14-2ubuntu2 libpython2.7-dev_2.7.14-2ubuntu2 libpython2.7-minimal_2.7.14-2ubuntu2 libpython2.7-stdlib_2.7.14-2ubuntu2 libpython3-all-dev_3.6.3-2 libpython3-dev_3.6.3-2 libpython3-stdlib_3.6.3-2 libpython3.6_3.6.3-1ubuntu1 libpython3.6-dev_3.6.3-1ubuntu1 libpython3.6-minimal_3.6.3-1ubuntu1 libpython3.6-stdlib_3.6.3-1ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu1 libseccomp2_2.3.1-2.1ubuntu3 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.1-0ubuntu5 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.0.0_1.0.2g-1ubuntu14 libstdc++-7-dev_7.2.0-13ubuntu1 libstdc++6_7.2.0-13ubuntu1 libsystemd0_235-2ubuntu2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_7.2.0-13ubuntu1 libubsan0_7.2.0-13ubuntu1 libudev1_235-2ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu5 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-5ubuntu2 linux-libc-dev_4.13.0-16.19 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.30.1-0ubuntu5 multiarch-support_2.26-0ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu14 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.1-2ubuntu1 perl-base_5.26.1-2ubuntu1 perl-modules-5.26_5.26.1-2ubuntu1 pinentry-curses_1.0.0-3 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.14-2ubuntu1 python-all_2.7.14-2ubuntu1 python-all-dev_2.7.14-2ubuntu1 python-dev_2.7.14-2ubuntu1 python-minimal_2.7.14-2ubuntu1 python-pkg-resources_36.6.0-1 python-py_1.4.34-3 python-pytest_3.2.1-2 python-setuptools_36.6.0-1 python2.7_2.7.14-2ubuntu2 python2.7-dev_2.7.14-2ubuntu2 python2.7-minimal_2.7.14-2ubuntu2 python3_3.6.3-2 python3-all_3.6.3-2 python3-all-dev_3.6.3-2 python3-dev_3.6.3-2 python3-minimal_3.6.3-2 python3-pkg-resources_36.6.0-1 python3-py_1.4.34-3 python3-pytest_3.2.1-2 python3-setuptools_36.6.0-1 python3.6_3.6.3-1ubuntu1 python3.6-dev_3.6.3-1ubuntu1 python3.6-minimal_3.6.3-1ubuntu1 readline-common_7.0-0ubuntu2 samtools_1.5-1build1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_235-2ubuntu2 systemd-sysv_235-2ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tabix_1.5-3 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Nov 10 19:15:13 2017 UTC gpgv: using RSA key gpgv: issuer "mattia@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.12.0.1+ds-4.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.12.0.1+ds dpkg-source: info: unpacking python-pysam_0.12.0.1+ds.orig.tar.gz dpkg-source: info: unpacking python-pysam_0.12.0.1+ds-4.debian.tar.xz dpkg-source: info: applying execute-linking-tests-only-when-explicitely-reque.patch dpkg-source: info: applying rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch dpkg-source: info: applying xfail.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-13709260 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13709260 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13709260 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.12.0.1+ds-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build python-pysam-0.12.0.1+ds dpkg-buildpackage: info: host architecture ppc64el fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.12.0.1+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.12.0.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.12.0.1+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.12.0.1+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi dh clean --with python2,python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.12.0.1+ds' dh_auto_clean I: pybuild base:184: python2.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-ppc64el' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:184: python3.6 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-ppc64el' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>/python-pysam-0.12.0.1+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild 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:184: python2.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.6 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/version.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/config.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcsamtools.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c building 'pysam.libchtslib' extension creating build creating build/temp.linux-ppc64el-2.7 creating build/temp.linux-ppc64el-2.7/pysam powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-ppc64el-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libchtslib.c:4: pysam/libchtslib.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libchtslib.c:1627:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libchtslib.o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c building 'pysam.libcsamfile' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-ppc64el-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcsamfile.c:4: pysam/libcsamfile.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcsamfile.c:1946:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-ppc64el-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcsamfile.o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o build/temp.linux-ppc64el-2.7/pysam/samfile_util.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c building 'pysam.libcalignmentfile' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-ppc64el-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcalignmentfile.c:4: pysam/libcalignmentfile.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcalignmentfile.c:2343:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:24737:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:23162:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:8785:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-ppc64el-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcalignmentfile.o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o build/temp.linux-ppc64el-2.7/pysam/samfile_util.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c building 'pysam.libcalignedsegment' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-ppc64el-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcalignedsegment.c:4: pysam/libcalignedsegment.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcalignedsegment.c:2814:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-ppc64el-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcalignedsegment.o build/temp.linux-ppc64el-2.7/pysam/htslib_util.o build/temp.linux-ppc64el-2.7/pysam/samfile_util.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabix.pyx to pysam/libctabix.c building 'pysam.libctabix' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-ppc64el-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libctabix.c:4: pysam/libctabix.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libctabix.c:2270:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8168:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_2tabix_index’: pysam/libctabix.c:13112:39: warning: overflow in implicit constant conversion [-Woverflow] __pyx_t_8 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 918, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:13144:39: warning: overflow in implicit constant conversion [-Woverflow] __pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 919, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:13446:43: warning: overflow in implicit constant conversion [-Woverflow] __pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 943, __pyx_L1_error) ^~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-ppc64el-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libctabix.o build/temp.linux-ppc64el-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c building 'pysam.libctabixproxies' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-ppc64el-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libctabixproxies.c:4: pysam/libctabixproxies.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libctabixproxies.c:1639:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libctabixproxies.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN cythoning pysam/libcvcf.pyx to pysam/libcvcf.c warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libcvcf' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-ppc64el-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcvcf.c:4: pysam/libcvcf.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcvcf.c:2203:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.69’: pysam/libcvcf.c:24706:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcvcf.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcf.pyx to pysam/libcbcf.c building 'pysam.libcbcf' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-ppc64el-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcbcf.c:4: pysam/libcbcf.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcbcf.c:2716:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:32796:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5:0, from pysam/libcbcf.c:489: /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) ^~~~~~~~~~~~~~~~ powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcbcf.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c building 'pysam.libcbgzf' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-ppc64el-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcbgzf.c:4: pysam/libcbgzf.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcbgzf.c:1206:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcbgzf.o -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c building 'pysam.libcfaidx' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-ppc64el-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcfaidx.c:4: pysam/libcfaidx.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcfaidx.c:1684:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c building 'pysam.libcsamtools' extension creating build/temp.linux-ppc64el-2.7/samtools powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-ppc64el-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam.c.pysam.c: In function ‘bam_view1’: samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0; ^ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam2bcf.c.pysam.c: In function ‘bcf_call_combine’: samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[4]’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (j=0; jn_alleles; j++) adr_out[j] = tmp[j]; ~~~~~~~~~~~^~~~~~~~ samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[3]’ may be used uninitialized in this function [-Wmaybe-uninitialized] samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-ppc64el-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcsamtools.o build/temp.linux-ppc64el-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_view.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bedcov.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/padding.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_import.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/faidx.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_split.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_index.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/phase.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/cut_target.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_color.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/dict.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sample.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_md.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bedidx.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bamtk.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_header.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/stats.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_plbuf.c.pysam.o -Lpysam -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c building 'pysam.libcbcftools' extension creating build/temp.linux-ppc64el-2.7/bcftools powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-ppc64el-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/filter.c.pysam.c: In function ‘filters_set_info_int’: bcftools/filter.c.pysam.c:430:28: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized] tok->values[0] = value; ~~~~~~~~~~~~~~~^~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/bam2bcf.c.pysam.c: In function ‘bcf_call_combine’: bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[4]’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (j=0; jn_alleles; j++) adr_out[j] = tmp[j]; ~~~~~~~~~~~^~~~~~~~ bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[3]’ may be used uninitialized in this function [-Wmaybe-uninitialized] bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function ‘init_data’, inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:810:5: bcftools/vcfcall.c.pysam.c:423:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] args->aux.ploidy = (uint8_t*) malloc(args->nsamples); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29:0, from /usr/include/htslib/vcf.h:40, from bcftools/vcfcall.c.pysam.c:34: bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’: /usr/include/stdlib.h:424:14: note: in a call to allocation function ‘malloc’ declared here extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur; ^~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-ppc64el-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcbcftools.o build/temp.linux-ppc64el-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/convert.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/prob1.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/consensus.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/version.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/tabix.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/kmin.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/ccall.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/filter.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/bin.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/HMM.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/csq.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/hclust.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/mcall.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/main.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/em.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/regidx.c.pysam.o -Lpysam -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcutils.pyx to pysam/libcutils.c building 'pysam.libcutils' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-ppc64el-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/python2.7/Python.h:78:0, from pysam/libcutils.c:4: pysam/libcutils.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ pysam/libcutils.c:1369:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:10757:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5606:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-ppc64el-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-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-YLnTZL/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -fexceptions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-2.7/pysam/libcutils.o build/temp.linux-ppc64el-2.7/pysam/pysam_util.o -Lpysam -L/usr/lib/powerpc64le-linux-gnu -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN I: pybuild base:184: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/version.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/config.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcsamtools.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools creating /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-ppc64el-3.6 creating build/temp.linux-ppc64el-3.6/pysam powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libchtslib.c -o build/temp.linux-ppc64el-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libchtslib.o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcsamfile.c -o build/temp.linux-ppc64el-3.6/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-ppc64el-3.6/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcsamfile.o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o build/temp.linux-ppc64el-3.6/pysam/samfile_util.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignmentfile.c -o build/temp.linux-ppc64el-3.6/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:24737:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:23162:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:8785:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-ppc64el-3.6/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcalignmentfile.o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o build/temp.linux-ppc64el-3.6/pysam/samfile_util.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignedsegment.c -o build/temp.linux-ppc64el-3.6/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-ppc64el-3.6/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcalignedsegment.o build/temp.linux-ppc64el-3.6/pysam/htslib_util.o build/temp.linux-ppc64el-3.6/pysam/samfile_util.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libctabix.c -o build/temp.linux-ppc64el-3.6/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8168:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_2tabix_index’: pysam/libctabix.c:13112:39: warning: overflow in implicit constant conversion [-Woverflow] __pyx_t_8 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 918, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:13144:39: warning: overflow in implicit constant conversion [-Woverflow] __pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 919, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:13446:43: warning: overflow in implicit constant conversion [-Woverflow] __pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 943, __pyx_L1_error) ^~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/tabix_util.c -o build/temp.linux-ppc64el-3.6/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libctabix.o build/temp.linux-ppc64el-3.6/pysam/tabix_util.o -Lpysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c pysam/libctabixproxies.c -o build/temp.linux-ppc64el-3.6/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libctabixproxies.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcvcf.c -o build/temp.linux-ppc64el-3.6/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.71’: pysam/libcvcf.c:24706:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcvcf.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbcf.c -o build/temp.linux-ppc64el-3.6/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:32796:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5:0, from pysam/libcbcf.c:489: /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) ^~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcbcf.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbgzf.c -o build/temp.linux-ppc64el-3.6/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcbgzf.o -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbgzf.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcfaidx.c -o build/temp.linux-ppc64el-3.6/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcfaidx.o -Lpysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) building 'pysam.libcsamtools' extension creating build/temp.linux-ppc64el-3.6/samtools powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcsamtools.c -o build/temp.linux-ppc64el-3.6/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_view.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedcov.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/padding.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_import.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/faidx.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_split.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam.c.pysam.c: In function ‘bam_view1’: samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0; ^ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_index.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/phase.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/cut_target.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_color.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/dict.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam2bcf.c.pysam.c: In function ‘bcf_call_combine’: samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[4]’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (j=0; jn_alleles; j++) adr_out[j] = tmp[j]; ~~~~~~~~~~~^~~~~~~~ samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[3]’ may be used uninitialized in this function [-Wmaybe-uninitialized] samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] samtools/bam2bcf.c.pysam.c:649:62: warning: ‘tmp[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sample.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_md.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedidx.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamtk.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_header.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-ppc64el-3.6/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcsamtools.o build/temp.linux-ppc64el-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_view.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bedcov.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_utils.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/padding.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_cat.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_import.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/faidx.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_split.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_quickcheck.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_index.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/phase.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/cut_target.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_color.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/dict.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam2bcf.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sample.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_md.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bedidx.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bamtk.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_header.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/stats.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_plbuf.c.pysam.o -Lpysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamtools.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) building 'pysam.libcbcftools' extension creating build/temp.linux-ppc64el-3.6/bcftools powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbcftools.c -o build/temp.linux-ppc64el-3.6/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/convert.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/prob1.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/consensus.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/version.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tabix.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/kmin.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ccall.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/filter.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/filter.c.pysam.c: In function ‘filters_set_info_int’: bcftools/filter.c.pysam.c:430:28: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized] tok->values[0] = value; ~~~~~~~~~~~~~~~^~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bin.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/HMM.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/csq.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/bam2bcf.c.pysam.c: In function ‘bcf_call_combine’: bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[4]’ may be used uninitialized in this function [-Wmaybe-uninitialized] for (j=0; jn_alleles; j++) adr_out[j] = tmp[j]; ~~~~~~~~~~~^~~~~~~~ bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[3]’ may be used uninitialized in this function [-Wmaybe-uninitialized] bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] bcftools/bam2bcf.c.pysam.c:672:62: warning: ‘tmp[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/hclust.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/mcall.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/main.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/em.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/regidx.c.pysam.c -o build/temp.linux-ppc64el-3.6/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcbcftools.o build/temp.linux-ppc64el-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfannotate.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfcnv.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/convert.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfbuf.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/smpl_ilist.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/prob1.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/consensus.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/version.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfnorm.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/tabix.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/kmin.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/ccall.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/filter.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfconcat.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/bin.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/HMM.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfindex.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfisec.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/csq.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/bam2bcf.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfcall.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/mpileup.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/hclust.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/bam_sample.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/mcall.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/main.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/em.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/regidx.c.pysam.o -Lpysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcftools.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcutils.c -o build/temp.linux-ppc64el-3.6/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:304:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^~~~~~~~~~~~~~~ pysam/libcutils.c:5606:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ powerpc64le-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/pysam_util.c -o build/temp.linux-ppc64el-3.6/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement powerpc64le-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O3 -fdebug-prefix-map=/<>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-ppc64el-3.6/pysam/libcutils.o build/temp.linux-ppc64el-3.6/pysam/pysam_util.o -Lpysam -L/<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-powerpc64le-linux-gnu -lcsamtools.cpython-36m-powerpc64le-linux-gnu -lcbcftools.cpython-36m-powerpc64le-linux-gnu -o /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.cpython-36m-powerpc64le-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-pysam-0.12.0.1+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.12.0.1+ds/tests/pysam_data' samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view -bS ex2.sam > ex2.bam samtools index ex2.bam samtools view -buS ex2.sam > uncompressed.bam samtools view -bS tag_bug.sam > tag_bug.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam samtools view -bS test_unaligned.sam > test_unaligned.bam samtools view -bS ex10.sam > ex10.bam samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam samtools view -bS example_empty_header.sam > example_empty_header.bam samtools view -bS ex9_fail.sam > ex9_fail.bam samtools view -bS issue100.sam > issue100.bam samtools view -bS ex5.sam > ex5.bam samtools view -bS ex6.sam > ex6.bam samtools view -bS rg_with_tab.sam > rg_with_tab.bam samtools view -bS ex_spliced.sam > ex_spliced.bam samtools view -bS ex9_nofail.sam > ex9_nofail.bam samtools view -bS example_btag.sam > example_btag.bam samtools view -bS test_query_position.sam > test_query_position.bam touch tmp.list samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam rm -f tmp.list samtools view -bS ex4.sam > ex4.bam samtools view -bS example_user_header.sam > example_user_header.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS ex3.sam > ex3.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index example_empty_with_header.bam samtools index test_unaligned.bam samtools index ex10.bam samtools index example_aligned_pairs.bam samtools index example_empty_header.bam samtools index ex9_fail.bam samtools index issue100.bam samtools index ex5.bam samtools index ex6.bam samtools index rg_with_tab.bam samtools index ex_spliced.bam samtools index ex9_nofail.bam samtools index example_btag.bam samtools index test_query_position.bam samtools index example_unmapped_reads_no_sq.bam samtools index ex4.bam samtools index example_user_header.bam samtools index ex8.bam samtools index ex3.bam samtools view -bC -T ex1.fa ex1.sam > ex1.cram samtools view -bC -T ex1.fa ex2.sam > ex2.cram samtools view -bC -T ex1.fa ex3.sam > ex3.cram samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai head -c 124000 ex2.bam > ex2_truncated.bam grep "^@" ex2.sam | samtools view -Sb - > empty.bam samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam make[2]: Leaving directory '/<>/python-pysam-0.12.0.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.12.0.1+ds/tests/cbcf_data' bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf make[2]: Leaving directory '/<>/python-pysam-0.12.0.1+ds/tests/cbcf_data' dh_auto_test I: pybuild base:184: cd /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m pytest tests ============================= test session starts ============================== platform linux2 -- Python 2.7.14, pytest-3.2.1, py-1.4.34, pluggy-0.4.0 -- /usr/bin/python2.7 cachedir: ../../../.cache rootdir: /<>/python-pysam-0.12.0.1+ds, inifile: setup.cfg collecting ... In file included from /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c:490:0: /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int hts_get_verbosity(); ^~~ In file included from /usr/include/python2.7/Python.h:78:0, from /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c:4: /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c: In function ‘newarrayobject’: /usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) ) ^ /usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’ : malloc((n) ? (n) : 1)) ^ /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c:2089:28: note: in expansion of macro ‘PyMem_NEW’ op->data.ob_item = PyMem_NEW(char, nbytes); ^~~~~~~~~ collected 779 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestAsString::testAsString PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM <- ../../../usr/lib/python2.7/unittest/case.py PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestTagParsing::testArrayTags PASSED tests/AlignmentFile_test.py::TestTagParsing::testCigar PASSED tests/AlignmentFile_test.py::TestTagParsing::testCigarString PASSED tests/AlignmentFile_test.py::TestTagParsing::testLongTags PASSED tests/AlignmentFile_test.py::TestTagParsing::testNegativeIntegers PASSED tests/AlignmentFile_test.py::TestTagParsing::testNegativeIntegers2 PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestHeaderSAM::testHeaders PASSED tests/AlignmentFile_test.py::TestHeaderSAM::testNameMapping PASSED tests/AlignmentFile_test.py::TestHeaderBAM::testHeaders PASSED tests/AlignmentFile_test.py::TestHeaderBAM::testNameMapping PASSED tests/AlignmentFile_test.py::TestHeaderCRAM::testHeaders PASSED tests/AlignmentFile_test.py::TestHeaderCRAM::testNameMapping PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestHeaderWriteRead::test_BAM PASSED tests/AlignmentFile_test.py::TestHeaderWriteRead::test_CRAM PASSED tests/AlignmentFile_test.py::TestHeaderWriteRead::test_SAM PASSED tests/AlignmentFile_test.py::TestUnmappedReads::testBAM PASSED tests/AlignmentFile_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFile_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFile_test.py::TestPileupObjects::testPileupRead PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegion PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegion PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegion PASSED tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPView PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestPileup::testAllStepper PASSED tests/AlignmentFile_test.py::TestPileup::testSamtoolsStepper PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFilePathIndex::testGarbageIndex PASSED tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithOtherIndex PASSED tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithStandardIndex PASSED tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithoutIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testGarbageIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithOtherIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithStandardIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithoutIndex PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] PL should be declared as Number=G [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/tabix_test.py::TestRemoteFileHTTP::testHeader PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testSetting PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testSetting PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== .pybuild/pythonX.Y_2.7/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/AlignmentFile_test.py:1865: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: http://doc.pytest.org/en/latest/warnings.html ============= 769 passed, 10 skipped, 1 warnings in 66.33 seconds ============== I: pybuild base:184: cd /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build; python3.6 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.6.3, pytest-3.2.1, py-1.4.34, pluggy-0.4.0 -- /usr/bin/python3.6 cachedir: ../../../.cache rootdir: /<>/python-pysam-0.12.0.1+ds, inifile: setup.cfg collecting ... In file included from /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/tests/_compile_test.c:490:0: /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int hts_get_verbosity(); ^~~ collected 783 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestAsString::testAsString PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM <- ../../../usr/lib/python3.6/unittest/case.py PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFile_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestTagParsing::testArrayTags PASSED tests/AlignmentFile_test.py::TestTagParsing::testCigar PASSED tests/AlignmentFile_test.py::TestTagParsing::testCigarString PASSED tests/AlignmentFile_test.py::TestTagParsing::testLongTags PASSED tests/AlignmentFile_test.py::TestTagParsing::testNegativeIntegers PASSED tests/AlignmentFile_test.py::TestTagParsing::testNegativeIntegers2 PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestHeaderSAM::testHeaders PASSED tests/AlignmentFile_test.py::TestHeaderSAM::testNameMapping PASSED tests/AlignmentFile_test.py::TestHeaderBAM::testHeaders PASSED tests/AlignmentFile_test.py::TestHeaderBAM::testNameMapping PASSED tests/AlignmentFile_test.py::TestHeaderCRAM::testHeaders PASSED tests/AlignmentFile_test.py::TestHeaderCRAM::testNameMapping PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestHeaderWriteRead::test_BAM PASSED tests/AlignmentFile_test.py::TestHeaderWriteRead::test_CRAM PASSED tests/AlignmentFile_test.py::TestHeaderWriteRead::test_SAM PASSED tests/AlignmentFile_test.py::TestUnmappedReads::testBAM PASSED tests/AlignmentFile_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFile_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFile_test.py::TestPileupObjects::testPileupRead PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegion PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegion PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegion PASSED tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPView PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestPileup::testAllStepper PASSED tests/AlignmentFile_test.py::TestPileup::testSamtoolsStepper PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFilePathIndex::testGarbageIndex PASSED tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithOtherIndex PASSED tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithStandardIndex PASSED tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithoutIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testGarbageIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithOtherIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithStandardIndex PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithoutIndex PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/tabix_test.py::TestRemoteFileHTTP::testHeader PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testSetting PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testSetting PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== .pybuild/pythonX.Y_3.6/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/tests/AlignmentFile_test.py:1865: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: http://doc.pytest.org/en/latest/warnings.html ============== 774 passed, 9 skipped, 1 warnings in 74.88 seconds ============== make[1]: Leaving directory '/<>/python-pysam-0.12.0.1+ds' 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 dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py install --root /<>/python-pysam-0.12.0.1+ds/debian/python-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7 creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/log.txt -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_stream.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamtools_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/samfile_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/namedtuple.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcftools.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/smpl_ilist.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/mw.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/hclust.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/regidx.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/bam_sample.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/bin.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/config.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/vcfbuf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/kheap.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/__init__.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/bcftools.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamtools.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcftools.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/tabix_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamtools.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcftools_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/bcftools.py -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/namedtuple.py to namedtuple.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc running install_egg_info running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'tests/pysam_data' warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.12.0.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:184: /usr/bin/python3 setup.py install --root /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6 creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/log.txt -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/pysam_stream.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/pysam_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/csamtools_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamtools.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/samfile_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcftools.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/htslib_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbgzf.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/smpl_ilist.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/mw.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/hclust.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/regidx.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/bam_sample.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/bin.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/config.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/vcfbuf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/kheap.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/__init__.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/pysam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcftools.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/tabix_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.cpython-36m-powerpc64le-linux-gnu.so -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamtools.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/cbcftools_util.h -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam creating /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/Pileup.cpython-36.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/version.cpython-36.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/samtools.cpython-36.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/config.cpython-36.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/utils.cpython-36.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/bcftools.cpython-36.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/__init__.cpython-36.pyc -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__init__.py to __init__.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/version.py to version.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/namedtuple.py to namedtuple.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/Pileup.py to Pileup.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/samtools.py to samtools.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/__init__.py to __init__.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/config.py to config.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/utils.py to utils.cpython-36.pyc byte-compiling /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/bcftools.py to bcftools.cpython-36.pyc running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'tests/pysam_data' warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.12.0.1+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam-0.12.0.1.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>/python-pysam-0.12.0.1+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.12.0.1+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[2]: Leaving directory '/<>/python-pysam-0.12.0.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.12.0.1+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/<>/python-pysam-0.12.0.1+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi dh_install -Xtest.gtf.gz make[1]: Leaving directory '/<>/python-pysam-0.12.0.1+ds' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python2 -a -O--buildsystem=pybuild I: dh_python2 fs:322: renaming libcalignedsegment.so to libcalignedsegment.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcalignmentfile.so to libcalignmentfile.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcbcf.so to libcbcf.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcbcftools.so to libcbcftools.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcbgzf.so to libcbgzf.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcfaidx.so to libcfaidx.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libchtslib.so to libchtslib.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcsamfile.so to libcsamfile.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcsamtools.so to libcsamtools.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libctabix.so to libctabix.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libctabixproxies.so to libctabixproxies.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcutils.so to libcutils.powerpc64le-linux-gnu.so I: dh_python2 fs:322: renaming libcvcf.so to libcvcf.powerpc64le-linux-gnu.so dh_python3 -a -O--buildsystem=pybuild dh_lintian -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_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-pysam: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions} dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam (in debian/python-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-pysam/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam-dbgsym (in debian/.debhelper/python-pysam/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python-pysam/DEBIAN/control, package python-pysam, directory debian/python-pysam pkgstripfiles: Truncating usr/share/doc/python-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/.debhelper/python3-pysam/dbgsym-root/DEBIAN/control, package python3-pysam-dbgsym, directory debian/.debhelper/python3-pysam/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam-dbgsym ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam ... pkgstripfiles: No PNG files. pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.12.0.1+ds-4_ppc64el.deb'. dpkg-deb: building package 'python-pysam' in '../python-pysam_0.12.0.1+ds-4_ppc64el.deb'. Renaming python3-pysam-dbgsym_0.12.0.1+ds-4_ppc64el.deb to python3-pysam-dbgsym_0.12.0.1+ds-4_ppc64el.ddeb pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python-pysam/dbgsym-root/DEBIAN/control, package python-pysam-dbgsym, directory debian/.debhelper/python-pysam/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam-dbgsym ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam dpkg-deb: building package 'python-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pysam/python-pysam-dbgsym_0.12.0.1+ds-4_ppc64el.deb'. pkgstripfiles: Truncating usr/share/doc/python3-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.12.0.1+ds-4_ppc64el.deb'. Renaming python-pysam-dbgsym_0.12.0.1+ds-4_ppc64el.deb to python-pysam-dbgsym_0.12.0.1+ds-4_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../python-pysam_0.12.0.1+ds-4_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build python-pysam-0.12.0.1+ds dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171110-2342 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.12.0.1+ds-4_ppc64el.changes: ------------------------------------------- Format: 1.8 Date: Fri, 10 Nov 2017 12:56:10 +0100 Source: python-pysam Binary: python-pysam python3-pysam python-pysam-tests Architecture: ppc64el Version: 0.12.0.1+ds-4 Distribution: bionic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Mattia Rizzolo Description: python-pysam - interface for the SAM/BAM sequence alignment and mapping format ( python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format ( python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Closes: 879867 Changes: python-pysam (0.12.0.1+ds-4) unstable; urgency=medium . * Team upload. * Revert "Skip tests on ppc64el to avoid build-dep on bcftools currently uninstallable". It seems to be installable now, and anyway now that the python3 transition is done we should fix it properly anyway. * d/control: + Bump the libhts-dev buil-dep to 1.5-3, to make sure we gain appropriate versioned symbols and therefore an appropriate versioned dependency on libhts2. Closes: #879867 + Bump Standards-Version to 4.1.1. 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It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 2. drwxr-xr-x root/root 0 2017-11-10 11:56 ./ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/python2.7/dist-packages/ -rw-r--r-- root/root 0 2017-11-10 11:56 ./usr/lib/python2.7/dist-packages/log.txt drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/ -rw-r--r-- root/root 1182 2017-11-10 11:56 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-11-10 11:56 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2017-11-10 11:56 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/not-zip-safe -rw-r--r-- root/root 6 2017-11-10 11:56 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/top_level.txt drwxr-xr-x root/root 0 2017-11-10 11:56 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./usr/share/doc/python-pysam/changelog.Debian.gz -rw-r--r-- root/root 6835 2017-11-10 11:52 ./usr/share/doc/python-pysam/copyright drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 211 2017-11-10 11:52 ./usr/share/lintian/overrides/python-pysam python3-pysam_0.12.0.1+ds-4_ppc64el.deb --------------------------------------- new debian package, version 2.0. size 1408020 bytes: control archive=3400 bytes. 786 bytes, 17 lines control 8697 bytes, 91 lines md5sums 172 bytes, 9 lines * postinst #!/bin/sh 401 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.12.0.1+ds-4 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7083 Depends: libc6 (>= 2.17), libhts2 (>= 1.5), zlib1g (>= 1:1.1.4), python3 (<< 3.7), python3 (>= 3.6~), python3:any (>= 3.3.2-2~) Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 3. drwxr-xr-x root/root 0 2017-11-10 11:56 ./ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/python3/ drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 0 2017-11-10 11:56 ./usr/lib/python3/dist-packages/log.txt drwxr-xr-x root/root 0 2017-11-10 11:56 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/ -rw-r--r-- root/root 1182 2017-11-10 11:56 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-11-10 11:56 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2017-11-10 11:56 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/not-zip-safe -rw-r--r-- root/root 6 2017-11-10 11:56 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/top_level.txt drwxr-xr-x root/root 0 2017-11-10 11:56 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./usr/share/lintian/overrides/ -rw-r--r-- root/root 209 2017-11-10 11:52 ./usr/share/lintian/overrides/python3-pysam +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 217292 Build-Time: 567 Distribution: bionic-proposed Host Architecture: ppc64el Install-Time: 25 Job: python-pysam_0.12.0.1+ds-4.dsc Machine Architecture: ppc64el Package: python-pysam Package-Time: 593 Source-Version: 0.12.0.1+ds-4 Space: 217292 Status: successful Version: 0.12.0.1+ds-4 -------------------------------------------------------------------------------- Finished at 20171110-2342 Build needed 00:09:53, 217292k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13709260 Scanning for processes to kill in build PACKAGEBUILD-13709260 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13709260 Stopping target for build PACKAGEBUILD-13709260 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13709260 Removing build PACKAGEBUILD-13709260