RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos01-ppc64el-027 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... 9 Nov 00:23:29 ntpdate[1772]: adjust time server 10.211.37.1 offset 0.003190 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13661251 /home/buildd/filecache-default/64ab4a3b1843816d631a3747c16f42fa2d8de59d Creating target for build PACKAGEBUILD-13661251 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13661251 Starting target for build PACKAGEBUILD-13661251 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13661251 '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-13661251 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13661251 Updating target for build PACKAGEBUILD-13661251 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 [7970 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4857 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el Packages [167 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [92.0 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el Packages [853 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [488 kB] Fetched 16.4 MB in 3s (4623 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 build-essential coreutils cpp-7 debconf dpkg dpkg-dev e2fslibs e2fsprogs findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcomerr2 libcurl3-gnutls libdpkg-perl libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libhogweed4 libitm1 libkeyutils1 libnettle6 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libubsan0 libudev1 linux-libc-dev multiarch-support openssl perl perl-base perl-modules-5.26 pinentry-curses systemd systemd-sysv sysvinit-utils tzdata 75 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 56.6 MB of archives. After this operation, 8716 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/main ppc64el coreutils ppc64el 8.26-3ubuntu4 [1251 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg ppc64el 1.19.0.4ubuntu1 [1149 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6-dev ppc64el 2.26-0ubuntu2 [2458 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-dev-bin ppc64el 2.26-0ubuntu2 [65.4 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main ppc64el linux-libc-dev ppc64el 4.13.0-16.19 [946 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgomp1 ppc64el 7.2.0-12ubuntu1 [69.3 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main ppc64el libitm1 ppc64el 7.2.0-12ubuntu1 [29.7 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main ppc64el gcc-7-base ppc64el 7.2.0-12ubuntu1 [18.3 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcc1 ppc64el 1:7.2.0-12ubuntu1 [29.7 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main ppc64el libatomic1 ppc64el 7.2.0-12ubuntu1 [8496 B] Get:12 http://ftpmaster.internal/ubuntu bionic/main ppc64el libasan4 ppc64el 7.2.0-12ubuntu1 [369 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main ppc64el liblsan0 ppc64el 7.2.0-12ubuntu1 [134 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtsan0 ppc64el 7.2.0-12ubuntu1 [289 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main ppc64el libubsan0 ppc64el 7.2.0-12ubuntu1 [136 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main ppc64el cpp-7 ppc64el 7.2.0-12ubuntu1 [6261 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcc1-0 ppc64el 7.2.0-12ubuntu1 [39.2 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main ppc64el g++-7 ppc64el 7.2.0-12ubuntu1 [7105 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main ppc64el gcc-7 ppc64el 7.2.0-12ubuntu1 [6898 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcc-7-dev ppc64el 7.2.0-12ubuntu1 [985 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main ppc64el libstdc++-7-dev ppc64el 7.2.0-12ubuntu1 [1526 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main ppc64el libstdc++6 ppc64el 7.2.0-12ubuntu1 [449 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgmp10 ppc64el 2:6.1.2+dfsg-1.1 [218 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libbinutils ppc64el 2.29.1-7ubuntu1 [457 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el binutils ppc64el 2.29.1-7ubuntu1 [3408 B] Get:26 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el binutils-common ppc64el 2.29.1-7ubuntu1 [190 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.29.1-7ubuntu1 [1968 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6 ppc64el 2.26-0ubuntu2 [2619 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el e2fslibs ppc64el 1.43.7-1 [173 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el e2fsprogs ppc64el 1.43.7-1 [510 kB] Get:31 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el findutils ppc64el 4.6.0+git+20170828-2 [314 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el perl-modules-5.26 all 5.26.1-2ubuntu1 [2760 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libperl5.26 ppc64el 5.26.1-2ubuntu1 [3405 kB] Get:34 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el perl ppc64el 5.26.1-2ubuntu1 [201 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el perl-base ppc64el 5.26.1-2ubuntu1 [1303 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main ppc64el base-passwd ppc64el 3.5.44 [50.1 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-bin ppc64el 2.26-0ubuntu2 [573 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main ppc64el sysvinit-utils ppc64el 2.88dsf-59.10ubuntu1 [20.6 kB] Get:39 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libudev1 ppc64el 235-2ubuntu2 [60.2 kB] Get:40 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libapt-pkg5.0 ppc64el 1.6~alpha4 [879 kB] Get:41 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgpg-error0 ppc64el 1.27-5 [42.1 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libgcrypt20 ppc64el 1.7.9-2 [440 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main ppc64el gpgv ppc64el 2.1.15-1ubuntu8 [218 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main ppc64el libseccomp2 ppc64el 2.3.1-2.1ubuntu3 [47.2 kB] Get:45 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el apt ppc64el 1.6~alpha4 [1191 kB] Get:46 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el debconf all 1.5.64 [124 kB] Get:47 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libapparmor1 ppc64el 2.11.0-2ubuntu18 [29.9 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap2 ppc64el 1:2.25-1.1 [13.7 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpcre3 ppc64el 2:8.39-5ubuntu3 [224 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libselinux1 ppc64el 2.7-2 [78.6 kB] Get:51 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el systemd ppc64el 235-2ubuntu2 [2959 kB] Get:52 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libsystemd0 ppc64el 235-2ubuntu2 [213 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el systemd-sysv ppc64el 235-2ubuntu2 [12.4 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap-ng0 ppc64el 0.7.7-3.1 [11.6 kB] Get:55 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libcomerr2 ppc64el 1.43.7-1 [11.6 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage-common all 2.7-2 [6916 B] Get:57 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage1 ppc64el 2.7-2 [85.4 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libss2 ppc64el 1.43.7-1 [11.4 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnettle6 ppc64el 3.3-2 [120 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhogweed4 ppc64el 3.3-2 [134 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main ppc64el libp11-kit0 ppc64el 0.23.9-2 [167 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main ppc64el pinentry-curses ppc64el 1.0.0-3 [37.5 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg ppc64el 2.1.15-1ubuntu8 [847 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg-agent ppc64el 2.1.15-1ubuntu8 [291 kB] Get:65 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libsqlite3-0 ppc64el 3.21.0-1 [464 kB] Get:66 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libssl1.0.0 ppc64el 1.0.2g-1ubuntu14 [880 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main ppc64el multiarch-support ppc64el 2.26-0ubuntu2 [6832 B] Get:68 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el openssl ppc64el 1.0.2g-1ubuntu14 [520 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main ppc64el tzdata all 2017c-1 [188 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main ppc64el libkeyutils1 ppc64el 1.5.9-9.1ubuntu1 [9896 B] Get:71 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpng16-16 ppc64el 1.6.34-1 [200 kB] Get:72 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el apt-transport-https all 1.6~alpha4 [1692 B] Get:73 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main ppc64el libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main ppc64el build-essential ppc64el 12.4ubuntu1 [4754 B] Get:76 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libpsl5 ppc64el 0.18.0-4 [42.6 kB] Get:77 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 56.6 MB in 2s (22.2 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 .../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.) Preparing to unpack .../dpkg_1.19.0.4ubuntu1_ppc64el.deb ... Unpacking dpkg (1.19.0.4ubuntu1) over (1.18.24ubuntu1) ... Setting up dpkg (1.19.0.4ubuntu1) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... 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Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 9 00:23:55 UTC 2017. Universal Time is now: Thu Nov 9 00:23:55 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (235-2ubuntu2) ... Setting up libubsan0:ppc64el (7.2.0-12ubuntu1) ... Setting up libtsan0:ppc64el (7.2.0-12ubuntu1) ... Setting up linux-libc-dev:ppc64el (4.13.0-16.19) ... Setting up perl-modules-5.26 (5.26.1-2ubuntu1) ... Setting up cpp-7 (7.2.0-12ubuntu1) ... Setting up liblsan0:ppc64el (7.2.0-12ubuntu1) ... Setting up binutils-common:ppc64el (2.29.1-7ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up libperl5.26:ppc64el (5.26.1-2ubuntu1) ... Setting up openssl (1.0.2g-1ubuntu14) ... Setting up libsqlite3-0:ppc64el (3.21.0-1) ... Setting up pinentry-curses (1.0.0-3) ... Setting up libc-dev-bin (2.26-0ubuntu2) ... Setting up libkeyutils1:ppc64el (1.5.9-9.1ubuntu1) ... Setting up gnupg-agent (2.1.15-1ubuntu8) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13661251 ppc64el bionic-proposed -c chroot:build-PACKAGEBUILD-13661251 --arch=ppc64el --dist=bionic-proposed --nolog python-pysam_0.12.0.1+ds-3.dsc Initiating build PACKAGEBUILD-13661251 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-027.buildd +==============================================================================+ | python-pysam 0.12.0.1+ds-3 (ppc64el) 09 Nov 2017 00:23 | +==============================================================================+ Package: python-pysam Version: 0.12.0.1+ds-3 Source Version: 0.12.0.1+ds-3 Distribution: bionic-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/python-pysam-pE4FqL/python-pysam-0.12.0.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-pE4FqL' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13661251/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.12.0.1+ds-3.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-zUmNzQ/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-zUmNzQ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zUmNzQ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-zUmNzQ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zUmNzQ/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-zUmNzQ/apt_archive ./ Packages [529 B] Fetched 2862 B in 0s (235 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-zUmNzQ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.5), python-pytest, python3-pytest Filtered Build-Depends: debhelper (>= 10), dh-exec, dh-python, libhts-dev (>= 1.5), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.5), python-pytest, python3-pytest dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-HlPHti/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-HlPHti/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HlPHti/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-HlPHti/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HlPHti/apt_archive ./ Sources [324 B] Get:5 copy:/<>/resolver-HlPHti/apt_archive ./ Packages [619 B] Fetched 3062 B in 0s (0 B/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 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 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 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, 82 newly installed, 1 to remove and 0 not upgraded. Need to get 68.0 MB of archives. After this operation, 227 MB of additional disk space will be used. Get:1 copy:/<>/resolver-HlPHti/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [944 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython3.6-minimal ppc64el 3.6.3-1ubuntu1 [532 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libexpat1 ppc64el 2.2.3-2 [88.6 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main ppc64el python3.6-minimal ppc64el 3.6.3-1ubuntu1 [1532 kB] Get:5 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python3-minimal ppc64el 3.6.3-2 [23.7 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main ppc64el mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main ppc64el libmpdec2 ppc64el 2.4.2-1 [82.6 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython3.6-stdlib ppc64el 3.6.3-1ubuntu1 [2140 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main ppc64el python3.6 ppc64el 3.6.3-1ubuntu1 [175 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libpython3-stdlib ppc64el 3.6.3-2 [7204 B] Get:11 http://ftpmaster.internal/ubuntu bionic/main ppc64el dh-python all 2.20170125 [83.7 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python3 ppc64el 3.6.3-2 [8768 B] Get:13 http://ftpmaster.internal/ubuntu bionic/main ppc64el groff-base ppc64el 1.22.3-9 [1361 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libbsd0 ppc64el 0.8.6-3 [50.0 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main ppc64el bsdmainutils ppc64el 9.0.12+nmu1ubuntu1 [179 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpipeline1 ppc64el 1.4.2-1 [23.6 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main ppc64el man-db ppc64el 2.7.6.1-2 [890 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython2.7-minimal ppc64el 2.7.14-2ubuntu2 [338 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main ppc64el python2.7-minimal ppc64el 2.7.14-2ubuntu2 [1439 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main ppc64el python-minimal ppc64el 2.7.14-2ubuntu1 [28.1 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython2.7-stdlib ppc64el 2.7.14-2ubuntu2 [2007 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main ppc64el python2.7 ppc64el 2.7.14-2ubuntu2 [233 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython-stdlib ppc64el 2.7.14-2ubuntu1 [7576 B] Get:24 http://ftpmaster.internal/ubuntu bionic/main ppc64el python ppc64el 2.7.14-2ubuntu1 [140 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main ppc64el libmagic-mgc ppc64el 1:5.32-1 [184 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main ppc64el libmagic1 ppc64el 1:5.32-1 [76.6 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main ppc64el file ppc64el 1:5.32-1 [22.7 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main ppc64el libglib2.0-0 ppc64el 2.54.1-1ubuntu1 [1160 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libicu60 ppc64el 60.1-1ubuntu2 [8339 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-5ubuntu2 [622 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main ppc64el gettext-base ppc64el 0.19.8.1-4ubuntu1 [49.5 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsigsegv2 ppc64el 2.11-1 [13.3 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main ppc64el m4 ppc64el 1.4.18-1 [202 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main ppc64el autoconf all 2.69-11 [322 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main ppc64el autotools-dev all 20161112.1+nmu1 [40.2 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main ppc64el automake all 1:1.15.1-3ubuntu1 [509 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main ppc64el autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:38 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el cython ppc64el 0.26.1-0.4 [1619 kB] Get:39 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el cython3 ppc64el 0.26.1-0.4 [1662 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtool all 2.4.6-2 [194 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main ppc64el dh-autoreconf all 14 [15.5 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main ppc64el libarchive-zip-perl all 1.59-1 [84.0 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main ppc64el libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtimedate-perl all 2.3000-2 [37.5 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main ppc64el dh-strip-nondeterminism all 0.040-1 [5196 B] Get:46 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcroco3 ppc64el 0.6.12-1 [74.4 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main ppc64el gettext ppc64el 0.19.8.1-4ubuntu1 [1142 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main ppc64el intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:49 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ppc64el 2.7.14-2ubuntu1 [7648 B] Get:59 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython-all-dev ppc64el 2.7.14-2ubuntu1 [1006 B] Get:60 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython3.6 ppc64el 3.6.3-1ubuntu1 [1536 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpython3.6-dev ppc64el 3.6.3-1ubuntu1 [3665 kB] Get:62 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libpython3-dev ppc64el 3.6.3-2 [7300 B] Get:63 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el libpython3-all-dev ppc64el 3.6.3-2 [1096 B] Get:64 http://ftpmaster.internal/ubuntu bionic/main ppc64el python-all ppc64el 2.7.14-2ubuntu1 [994 B] Get:65 http://ftpmaster.internal/ubuntu bionic/main ppc64el python2.7-dev ppc64el 2.7.14-2ubuntu2 [278 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main ppc64el python-dev ppc64el 2.7.14-2ubuntu1 [1176 B] Get:67 http://ftpmaster.internal/ubuntu bionic/main ppc64el python-all-dev ppc64el 2.7.14-2ubuntu1 [1016 B] Get:68 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python-pkg-resources all 36.6.0-1 [129 kB] Get:69 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el python-py all 1.4.34-3 [63.4 kB] Get:70 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el python-pytest all 3.2.1-2 [143 kB] Get:71 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python-setuptools all 36.6.0-1 [262 kB] Get:72 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python3-all ppc64el 3.6.3-2 [1072 B] Get:73 http://ftpmaster.internal/ubuntu bionic/main ppc64el python3.6-dev ppc64el 3.6.3-1ubuntu1 [519 kB] Get:74 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python3-dev ppc64el 3.6.3-2 [1280 B] Get:75 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python3-all-dev ppc64el 3.6.3-2 [1096 B] Get:76 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python3-pkg-resources all 36.6.0-1 [99.2 kB] Get:77 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el python3-py all 1.4.34-3 [63.5 kB] Get:78 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el python3-pytest all 3.2.1-2 [143 kB] Get:79 http://ftpmaster.internal/ubuntu bionic-proposed/main ppc64el python3-setuptools all 36.6.0-1 [180 kB] Get:80 http://ftpmaster.internal/ubuntu bionic-proposed/universe ppc64el samtools ppc64el 1.5-1build1 [291 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-0ubuntu2 [178 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main ppc64el dh-exec ppc64el 0.23build1 [24.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.0 MB in 2s (33.9 MB/s) (Reading database ... 12547 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package libpython3.6-minimal:ppc64el. (Reading database ... 12538 files and directories currently installed.) Preparing to unpack .../0-libpython3.6-minimal_3.6.3-1ubuntu1_ppc64el.deb ... Unpacking libpython3.6-minimal:ppc64el (3.6.3-1ubuntu1) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../1-libexpat1_2.2.3-2_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.2.3-2) ... Selecting previously unselected package python3.6-minimal. Preparing to unpack .../2-python3.6-minimal_3.6.3-1ubuntu1_ppc64el.deb ... Unpacking python3.6-minimal (3.6.3-1ubuntu1) ... Selecting previously unselected package python3-minimal. Preparing to unpack .../3-python3-minimal_3.6.3-2_ppc64el.deb ... Unpacking python3-minimal (3.6.3-2) ... Selecting previously unselected package mime-support. Preparing to unpack .../4-mime-support_3.60ubuntu1_all.deb ... Unpacking mime-support (3.60ubuntu1) ... 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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 (1.5-2) ... 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 (1.5-2) ... 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 (1.5-2) ... 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 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 ... 17754 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_7.2.0-12ubuntu1 gcc-7_7.2.0-12ubuntu1 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-12ubuntu1 libstdc++6_7.2.0-12ubuntu1 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 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_1:2.30.1-0ubuntu4 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_7.2.0-12ubuntu1 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_4.8.2 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_2.30.1-0ubuntu4 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1ubuntu1 g++-7_7.2.0-12ubuntu1 gcc_4:7.2.0-1ubuntu1 gcc-7_7.2.0-12ubuntu1 gcc-7-base_7.2.0-12ubuntu1 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_7.2.0-12ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-3 libatomic1_7.2.0-12ubuntu1 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_2.30.1-0ubuntu4 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_7.2.0-12ubuntu1 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_2.30.1-0ubuntu4 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-12ubuntu1 libgcc1_1:7.2.0-12ubuntu1 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_7.2.0-12ubuntu1 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_1.5-2 libhts2_1.5-2 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_7.2.0-12ubuntu1 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_7.2.0-12ubuntu1 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_2.30.1-0ubuntu4 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_2.30.1-0ubuntu4 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.0.0_1.0.2g-1ubuntu14 libstdc++-7-dev_7.2.0-12ubuntu1 libstdc++6_7.2.0-12ubuntu1 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_7.2.0-12ubuntu1 libubsan0_7.2.0-12ubuntu1 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_2.30.1-0ubuntu4 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_2.30.1-0ubuntu4 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_1.5-2 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu4 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 Tue Oct 24 16:55:17 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.12.0.1+ds-3.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-3.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-13661251 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13661251 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13661251 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-3 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/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/namedtuple.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 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/config.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/libcvcf.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/libcsamfile.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/libcutils.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/libctabix.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/libcsamtools.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/libcalignedsegment.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/cbcftools_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/pysam_stream.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/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 creating /<>/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/stats_isize.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/bam.h -> /<>/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/config.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_lpileup.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/bam_endian.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/sam_header.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 creating /<>/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/call.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/gvcf.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/config.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/HMM.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/bam_sample.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/vcfbuf.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/tsv2vcf.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/bin.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/mw.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/bcftools.h -> /<>/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/version.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/filter.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 creating /<>/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/zconf.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.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_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/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_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/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/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_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/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/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_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/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/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/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/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/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/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/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_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/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/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/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/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/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/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/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/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_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 -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_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_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/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/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/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/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/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/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/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/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_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 -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.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/padding.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_color.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/dict.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/phase.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_md.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_header.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/cut_target.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bedidx.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_index.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/stats.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_split.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bamtk.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_view.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bedcov.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/sample.c.pysam.o build/temp.linux-ppc64el-2.7/samtools/bam_quickcheck.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 -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/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 -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/vcfcnv.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/prob1.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/tabix.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/bin.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/consensus.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/hclust.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/ccall.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/version.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/HMM.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/vcfnorm.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/main.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/convert.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/em.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/filter.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/kmin.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/mcall.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/regidx.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/csq.c.pysam.o build/temp.linux-ppc64el-2.7/bcftools/vcfisec.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/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/namedtuple.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 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/config.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/libcvcf.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/libcsamfile.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/libcutils.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/libctabix.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/libcsamtools.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/libcalignedsegment.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/cbcftools_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/pysam_stream.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/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 creating /<>/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/stats_isize.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/bam.h -> /<>/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/config.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_lpileup.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/bam_endian.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/sam_header.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 creating /<>/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/call.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/gvcf.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/config.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/HMM.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/bam_sample.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/vcfbuf.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/tsv2vcf.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/bin.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/mw.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/bcftools.h -> /<>/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/version.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/filter.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 creating /<>/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/zconf.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/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/namedtuple.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/__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/config.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/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/namedtuple.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/__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/config.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.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_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/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_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/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/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_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/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/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_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/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/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/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/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/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/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/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_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/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/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/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/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/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/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/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/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_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 -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_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_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/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/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/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/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/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/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/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/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_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 -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.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/padding.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_color.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/dict.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/phase.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_md.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_utils.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam2bcf.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_header.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/cut_target.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bedidx.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_index.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_cat.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_plbuf.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/stats.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_split.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bamtk.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_view.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bedcov.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/sample.c.pysam.o build/temp.linux-ppc64el-3.6/samtools/bam_quickcheck.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 -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/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 -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/vcfcnv.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/prob1.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfannotate.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/tabix.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/bin.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/consensus.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/hclust.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfindex.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/ccall.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/version.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/HMM.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/vcfnorm.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/main.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/convert.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/em.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/mpileup.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/smpl_ilist.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/filter.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/kmin.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/bam_sample.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfbuf.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfconcat.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/mcall.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/regidx.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/csq.c.pysam.o build/temp.linux-ppc64el-3.6/bcftools/vcfisec.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 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 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/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/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/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/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/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/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/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/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/libcsamtools.so -> /<>/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/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/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/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/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/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/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/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_lpileup.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/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/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/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/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/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/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/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/bam2bcf.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/__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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/libctabix.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/libchtslib.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__.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/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/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/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/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/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/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/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/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/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/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/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_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/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/csamtools_util.h -> /<>/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/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/namedtuple.py to namedtuple.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 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/config.py to config.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 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/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/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/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/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/cbcftools_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/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/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/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/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/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/libcalignmentfile.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/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/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/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/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/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/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/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_lpileup.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/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/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/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/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/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/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/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/bam2bcf.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/__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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/libctabix.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/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/libchtslib.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/__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/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/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/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/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/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/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/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/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/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/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_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/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/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/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/libcvcf.cpython-36m-powerpc64le-linux-gnu.so -> /<>/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/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/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/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 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/config.py to config.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 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} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3: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 python-pysam-dbgsym (in debian/.debhelper/python-pysam/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-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/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgstripfiles: processing control file: debian/.debhelper/python-pysam/dbgsym-root/DEBIAN/control, package python-pysam-dbgsym, directory debian/.debhelper/python-pysam/dbgsym-root INFO: pkgstripfiles: waiting for lock (python3-pysam) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pysam/python-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.deb'. INFO: pkgstripfiles: waiting for lock (python3-pysam) ... Renaming python-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.deb to python-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... 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: 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: 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-3_ppc64el.deb'. pkgstripfiles: Truncating usr/share/doc/python-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Truncating usr/share/doc/python3-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam ... pkgstripfiles: No PNG files. pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam ... dpkg-deb: building package 'python-pysam' in '../python-pysam_0.12.0.1+ds-3_ppc64el.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.12.0.1+ds-3_ppc64el.deb'. Renaming python3-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.deb to python3-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../python-pysam_0.12.0.1+ds-3_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 20171109-0031 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.12.0.1+ds-3_ppc64el.changes: ------------------------------------------- Format: 1.8 Date: Tue, 24 Oct 2017 18:54:29 +0200 Source: python-pysam Binary: python-pysam python3-pysam python-pysam-tests Architecture: ppc64el Version: 0.12.0.1+ds-3 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 ( Changes: python-pysam (0.12.0.1+ds-3) unstable; urgency=medium . * Team upload. * Support DEB_BUILD_OPTIONS=nocheck. * Skip tests on ppc64el to avoid build-dep on bcftools which is currently uninstallable. Hopefully this will help unstuck the current python3 transition. Checksums-Sha1: e6bdd8a4e21b8adc11f72cc8dc2980e4de6065c7 4458720 python-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb 4e4c63c6314279734cc29eed1ad01010e0e6b0b7 8447 python-pysam_0.12.0.1+ds-3_ppc64el.buildinfo e683aa35057b9491029681cb226a25fd8ce88cf1 1383052 python-pysam_0.12.0.1+ds-3_ppc64el.deb e7ee9bcd5506078b85a204e45b517eedc0e2a8d4 5049564 python3-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb 7c7dc41ec9bf924596d9747f08aab9ed0e058815 1408596 python3-pysam_0.12.0.1+ds-3_ppc64el.deb Checksums-Sha256: 7a6596da838336235968b13887f285f2fcba4a20845054192d8158e0abda6199 4458720 python-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb f211a480c37bf61dd490a257feb8f86030a7a4a4bcc1d11e284e30eb55f5186f 8447 python-pysam_0.12.0.1+ds-3_ppc64el.buildinfo d8069b200963eb741cf479292719edc741314a7a39b2a8cfb6d364fd7d627b35 1383052 python-pysam_0.12.0.1+ds-3_ppc64el.deb 3958b7d2b8c859869c53cd72130505946ddeafac986683b9c28cf60d2c0f90c1 5049564 python3-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb 215bcb4c977295cb9019e5e92ed480a9fabd911a441fe4aa1b4f7b59400c636f 1408596 python3-pysam_0.12.0.1+ds-3_ppc64el.deb Files: 382e8aab10c0c6f61071e5d7777e2cbf 4458720 debug optional python-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb e3fc2dddb0de1eb453295442908952be 8447 python optional python-pysam_0.12.0.1+ds-3_ppc64el.buildinfo 0b34660ea6f6a1d4cb3633f9a99ecc91 1383052 python optional python-pysam_0.12.0.1+ds-3_ppc64el.deb 729e881d10858720fdea902b9389fb46 5049564 debug optional python3-pysam-dbgsym_0.12.0.1+ds-3_ppc64el.ddeb 0cb866b405a1d0bc73319619f48e80ac 1408596 python optional python3-pysam_0.12.0.1+ds-3_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-pysam_0.12.0.1+ds-3_ppc64el.deb -------------------------------------- new debian package, version 2.0. size 1383052 bytes: control archive=3292 bytes. 773 bytes, 16 lines control 8640 bytes, 90 lines md5sums 162 bytes, 9 lines * postinst #!/bin/sh 261 bytes, 14 lines * prerm #!/bin/sh Package: python-pysam Version: 0.12.0.1+ds-3 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6954 Depends: libc6 (>= 2.17), libhts2, zlib1g (>= 1:1.1.4), python (<< 2.8), python (>= 2.7~), python:any (<< 2.8), python:any (>= 2.7.5-5~) Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2) 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 2. drwxr-xr-x root/root 0 2017-10-24 16:54 ./ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/ -rw-r--r-- root/root 1182 2017-10-24 16:54 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-10-24 16:54 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2017-10-24 16:54 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/not-zip-safe -rw-r--r-- root/root 6 2017-10-24 16:54 ./usr/lib/python2.7/dist-packages/pysam-0.12.0.1.egg-info/top_level.txt drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python2.7/dist-packages/pysam/ -rw-r--r-- root/root 8305 2017-09-06 21:18 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./usr/lib/python2.7/dist-packages/pysam/include/bcftools/gvcf.h -rw-r--r-- root/root 2781 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/hclust.h -rw-r--r-- root/root 3163 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/khash_str2str.h -rw-r--r-- root/root 7499 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/kheap.h -rw-r--r-- root/root 1619 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/kmin.h -rw-r--r-- root/root 62247 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/mw.h -rw-r--r-- root/root 4409 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/ploidy.h -rw-r--r-- root/root 3551 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/prob1.h -rw-r--r-- root/root 151 2017-09-06 21:18 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/pysam.h -rw-r--r-- root/root 7538 2017-09-06 21:18 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./usr/share/doc/python-pysam/changelog.Debian.gz -rw-r--r-- root/root 6835 2017-10-24 15:44 ./usr/share/doc/python-pysam/copyright drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/share/lintian/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 211 2017-10-24 15:44 ./usr/share/lintian/overrides/python-pysam python3-pysam_0.12.0.1+ds-3_ppc64el.deb --------------------------------------- new debian package, version 2.0. size 1408596 bytes: control archive=3388 bytes. 777 bytes, 17 lines control 8625 bytes, 90 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-3 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7082 Depends: libc6 (>= 2.17), libhts2, 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 2017-10-24 16:54 ./ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python3/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/ -rw-r--r-- root/root 1182 2017-10-24 16:54 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-10-24 16:54 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2017-10-24 16:54 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/not-zip-safe -rw-r--r-- root/root 6 2017-10-24 16:54 ./usr/lib/python3/dist-packages/pysam-0.12.0.1.egg-info/top_level.txt drwxr-xr-x root/root 0 2017-10-24 16:54 ./usr/lib/python3/dist-packages/pysam/ -rw-r--r-- root/root 8305 2017-09-06 21:18 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21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/hclust.h -rw-r--r-- root/root 3163 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/khash_str2str.h -rw-r--r-- root/root 7499 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kheap.h -rw-r--r-- root/root 1619 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kmin.h -rw-r--r-- root/root 62247 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/mw.h -rw-r--r-- root/root 4409 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/ploidy.h -rw-r--r-- root/root 3551 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/prob1.h -rw-r--r-- root/root 151 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/pysam.h -rw-r--r-- root/root 7538 2017-09-06 21:18 ./usr/lib/python3/dist-packages/pysam/include/bcftools/rbuf.h -rw-r--r-- root/root 7190 2017-09-06 21:18 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 216488 Build-Time: 410 Distribution: bionic-proposed Host Architecture: ppc64el Install-Time: 23 Job: python-pysam_0.12.0.1+ds-3.dsc Machine Architecture: ppc64el Package: python-pysam Package-Time: 434 Source-Version: 0.12.0.1+ds-3 Space: 216488 Status: successful Version: 0.12.0.1+ds-3 -------------------------------------------------------------------------------- Finished at 20171109-0031 Build needed 00:07:14, 216488k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13661251 Scanning for processes to kill in build PACKAGEBUILD-13661251 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13661251 Stopping target for build PACKAGEBUILD-13661251 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13661251 Removing build PACKAGEBUILD-13661251