https://launchpad.net/ubuntu/+source/python-pysam/0.15.1+ds-1/+build/15634523 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-029 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:50:27 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 1 Jan 11:13:22 ntpdate[1840]: adjust time server 10.211.37.1 offset -0.485153 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15634523 /home/buildd/filecache-default/a8e076447bc9c859868a26138221e631724b6c90 Creating target for build PACKAGEBUILD-15634523 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15634523 Starting target for build PACKAGEBUILD-15634523 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15634523 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15634523 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15634523 Updating target for build PACKAGEBUILD-15634523 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main armhf Packages [958 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe armhf Packages [8701 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5177 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main armhf Packages [85.5 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [43.1 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf Packages [331 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [194 kB] Fetched 16.5 MB in 6s (2647 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt binutils binutils-arm-linux-gnueabihf binutils-common cpp-8 dash dpkg dpkg-dev e2fslibs e2fsprogs g++-8 gcc-8 gcc-8-base init init-system-helpers libapt-pkg5.0 libasan5 libassuan0 libatomic1 libbinutils libcc1-0 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libgcc-8-dev libgcc1 libgnutls30 libgomp1 libgpg-error0 libpng16-16 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libubsan1 libzstd1 linux-libc-dev sed tzdata 40 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 31.7 MB of archives. After this operation, 104 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main armhf dpkg armhf 1.19.2ubuntu2 [1056 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main armhf dash armhf 0.5.10.2-4 [78.3 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main armhf sed armhf 4.7-1 [181 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed/main armhf init-system-helpers all 1.56+nmu1 [38.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libgnutls30 armhf 3.6.5-2ubuntu1 [700 kB] Get:6 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libubsan1 armhf 8.2.0-13ubuntu1 [109 kB] Get:7 http://ftpmaster.internal/ubuntu disco-proposed/main armhf gcc-8-base armhf 8.2.0-13ubuntu1 [18.6 kB] Get:8 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libgcc1 armhf 1:8.2.0-13ubuntu1 [37.1 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libgomp1 armhf 8.2.0-13ubuntu1 [66.6 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libatomic1 armhf 8.2.0-13ubuntu1 [7048 B] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libasan5 armhf 8.2.0-13ubuntu1 [349 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main armhf cpp-8 armhf 8.2.0-13ubuntu1 [5640 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libcc1-0 armhf 8.2.0-13ubuntu1 [32.5 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main armhf g++-8 armhf 8.2.0-13ubuntu1 [6429 kB] Get:15 http://ftpmaster.internal/ubuntu disco-proposed/main armhf gcc-8 armhf 8.2.0-13ubuntu1 [6348 kB] Get:16 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libgcc-8-dev armhf 8.2.0-13ubuntu1 [631 kB] Get:17 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libstdc++-8-dev armhf 8.2.0-13ubuntu1 [1596 kB] Get:18 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libstdc++6 armhf 8.2.0-13ubuntu1 [349 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libbinutils armhf 2.31.1-11ubuntu1 [309 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main armhf binutils-common armhf 2.31.1-11ubuntu1 [194 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main armhf binutils armhf 2.31.1-11ubuntu1 [3348 B] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.31.1-11ubuntu1 [2150 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main armhf libzstd1 armhf 1.3.5+dfsg-2 [190 kB] Get:24 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libapt-pkg5.0 armhf 1.8.0~alpha3 [732 kB] Get:25 http://ftpmaster.internal/ubuntu disco-proposed/main armhf apt armhf 1.8.0~alpha3 [1113 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main armhf libext2fs2 armhf 1.44.5-1 [145 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main armhf e2fsprogs armhf 1.44.5-1 [492 kB] Get:28 http://ftpmaster.internal/ubuntu disco-proposed/main armhf init armhf 1.56+nmu1 [6080 B] Get:29 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libgpg-error0 armhf 1.33-3 [49.3 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main armhf libcom-err2 armhf 1.44.5-1 [8468 B] Get:31 http://ftpmaster.internal/ubuntu disco/main armhf libss2 armhf 1.44.5-1 [9324 B] Get:32 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libsqlite3-0 armhf 3.26.0+fossilbc891ac6b-1 [449 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main armhf tzdata all 2018i-1 [189 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libpng16-16 armhf 1.6.36-2 [162 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main armhf dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main armhf libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main armhf e2fslibs armhf 1.44.5-1 [2704 B] Get:38 http://ftpmaster.internal/ubuntu disco-proposed/main armhf libassuan0 armhf 2.5.2-1 [28.7 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main armhf libcomerr2 armhf 1.44.5-1 [2700 B] Get:40 http://ftpmaster.internal/ubuntu disco-proposed/main armhf linux-libc-dev armhf 4.19.0-9.10 [1024 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.7 MB in 1s (26.9 MB/s) (Reading database ... 12402 files and directories currently installed.) 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Setting up libss2:armhf (1.44.5-1) ... Setting up libcc1-0:armhf (8.2.0-13ubuntu1) ... Setting up e2fslibs:armhf (1.44.5-1) ... Setting up libpng16-16:armhf (1.6.36-2) ... Setting up tzdata (2018i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 1 11:13:52 UTC 2019. Universal Time is now: Tue Jan 1 11:13:52 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up init (1.56+nmu1) ... Setting up linux-libc-dev:armhf (4.19.0-9.10) ... Setting up libdpkg-perl (1.19.2ubuntu2) ... Setting up e2fsprogs (1.44.5-1) ... Setting up binutils-common:armhf (2.31.1-11ubuntu1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libsqlite3-0:armhf (3.26.0+fossilbc891ac6b-1) ... Setting up libcomerr2:armhf (1.44.5-1) ... Setting up libasan5:armhf (8.2.0-13ubuntu1) ... Setting up libassuan0:armhf (2.5.2-1) ... Setting up libubsan1:armhf (8.2.0-13ubuntu1) ... Setting up libbinutils:armhf (2.31.1-11ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.31.1-11ubuntu1) ... Setting up libgcc-8-dev:armhf (8.2.0-13ubuntu1) ... Setting up binutils (2.31.1-11ubuntu1) ... Setting up libstdc++-8-dev:armhf (8.2.0-13ubuntu1) ... Setting up gcc-8 (8.2.0-13ubuntu1) ... Setting up g++-8 (8.2.0-13ubuntu1) ... Setting up dpkg-dev (1.19.2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15634523 armhf disco-proposed -c chroot:build-PACKAGEBUILD-15634523 --arch=armhf --dist=disco-proposed --nolog python-pysam_0.15.1+ds-1.dsc Initiating build PACKAGEBUILD-15634523 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:50:27 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-029.buildd +==============================================================================+ | python-pysam 0.15.1+ds-1 (armhf) 01 Jan 2019 11:13 | +==============================================================================+ Package: python-pysam Version: 0.15.1+ds-1 Source Version: 0.15.1+ds-1 Distribution: disco-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/python-pysam-BE1dY6/python-pysam-0.15.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-BE1dY6' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15634523/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.15.1+ds-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-RrFgIj/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-RrFgIj/apt_archive ./ InRelease Get:2 copy:/<>/resolver-RrFgIj/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-RrFgIj/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-RrFgIj/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-RrFgIj/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (142 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-RrFgIj/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 ... 12406 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest Filtered Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-mytBDJ/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-mytBDJ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mytBDJ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-mytBDJ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mytBDJ/apt_archive ./ Sources [315 B] Get:5 copy:/<>/resolver-mytBDJ/apt_archive ./ Packages [625 B] Fetched 3059 B in 0s (144 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-pysam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-atomicwrites python-attr python-dev python-funcsigs python-minimal python-more-itertools python-pathlib2 python-pkg-resources python-pluggy python-py python-pytest python-scandir python-setuptools python-six python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-lib2to3 python3-minimal python3-more-itertools python3-pkg-resources python3-pluggy python3-py python3-pytest python3-setuptools python3-six python3.7 python3.7-dev python3.7-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python-attr-doc python-funcsigs-doc subversion python-pytest-xdist python-mock python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.7-venv python3.7-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-atomicwrites python-attr python-dev python-funcsigs python-minimal python-more-itertools python-pathlib2 python-pkg-resources python-pluggy python-py python-pytest python-scandir python-setuptools python-six python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-lib2to3 python3-minimal python3-more-itertools python3-pkg-resources python3-pluggy python3-py python3-pytest python3-setuptools python3-six python3.7 python3.7-dev python3.7-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 118 MB of archives. After this operation, 255 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu disco/main armhf python-setuptools all 40.6.2-1 [327 kB] Get:112 http://ftpmaster.internal/ubuntu disco/main armhf python3-all armhf 3.7.1-1ubuntu1 [1108 B] Get:113 http://ftpmaster.internal/ubuntu disco/main armhf python3.7-dev armhf 3.7.2~rc1-1 [510 kB] Get:114 http://ftpmaster.internal/ubuntu disco/main armhf python3-dev armhf 3.7.1-1ubuntu1 [1312 B] Get:115 http://ftpmaster.internal/ubuntu disco/main armhf python3-all-dev armhf 3.7.1-1ubuntu1 [1112 B] Get:116 http://ftpmaster.internal/ubuntu disco/universe armhf python3-atomicwrites all 1.1.5-2 [6932 B] Get:117 http://ftpmaster.internal/ubuntu disco/main armhf python3-attr all 18.2.0-1 [29.6 kB] Get:118 http://ftpmaster.internal/ubuntu disco-proposed/main armhf python3-six all 1.12.0-1 [11.7 kB] Get:119 http://ftpmaster.internal/ubuntu disco/universe armhf python3-more-itertools all 4.2.0-1 [39.3 kB] Get:120 http://ftpmaster.internal/ubuntu disco/main armhf python3-pkg-resources all 40.6.2-1 [99.6 kB] Get:121 http://ftpmaster.internal/ubuntu disco/universe armhf python3-pluggy all 0.8.0-1 [17.5 kB] Get:122 http://ftpmaster.internal/ubuntu disco/universe armhf python3-py all 1.7.0-1 [65.5 kB] Get:123 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf python3-pytest all 3.10.1-2 [166 kB] Get:124 http://ftpmaster.internal/ubuntu disco/main armhf python3-setuptools all 40.6.2-1 [251 kB] Get:125 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf samtools armhf 1.9-1 [387 kB] Get:126 http://ftpmaster.internal/ubuntu disco-proposed/universe armhf tabix armhf 1.9-8 [249 kB] Get:127 http://ftpmaster.internal/ubuntu disco/main armhf dh-exec armhf 0.23build1 [23.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 118 MB in 5s (24.1 MB/s) Selecting previously unselected package libpython3.7-minimal:armhf. 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Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-141-generic arm64 (armv7l) Toolchain package versions: binutils_2.31.1-11ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-13ubuntu1 gcc-8_8.2.0-13ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-13ubuntu1 libstdc++6_8.2.0-13ubuntu1 linux-libc-dev_4.19.0-9.10 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 bcftools_1.9-1 binutils_2.31.1-11ubuntu1 binutils-arm-linux-gnueabihf_2.31.1-11ubuntu1 binutils-common_2.31.1-11ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 coreutils_8.28-1ubuntu2 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ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-3 python-all_2.7.15-3 python-all-dev_2.7.15-3 python-atomicwrites_1.1.5-2 python-attr_18.2.0-1 python-dev_2.7.15-3 python-funcsigs_1.0.2-4 python-minimal_2.7.15-3 python-more-itertools_4.2.0-1 python-pathlib2_2.3.3-1 python-pkg-resources_40.6.2-1 python-pluggy_0.8.0-1 python-py_1.7.0-1 python-pytest_3.10.1-2 python-scandir_1.9.0-2 python-setuptools_40.6.2-1 python-six_1.12.0-1 python2_2.7.15-3 python2-dev_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-dev_2.7.15-5 python2.7-minimal_2.7.15-5 python3_3.7.1-1ubuntu1 python3-all_3.7.1-1ubuntu1 python3-all-dev_3.7.1-1ubuntu1 python3-atomicwrites_1.1.5-2 python3-attr_18.2.0-1 python3-dev_3.7.1-1ubuntu1 python3-distutils_3.7.1-1ubuntu4 python3-lib2to3_3.7.1-1ubuntu4 python3-minimal_3.7.1-1ubuntu1 python3-more-itertools_4.2.0-1 python3-pkg-resources_40.6.2-1 python3-pluggy_0.8.0-1 python3-py_1.7.0-1 python3-pytest_3.10.1-2 python3-setuptools_40.6.2-1 python3-six_1.12.0-1 python3.7_3.7.2~rc1-1 python3.7-dev_3.7.2~rc1-1 python3.7-minimal_3.7.2~rc1-1 readline-common_7.0-5 samtools_1.9-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tabix_1.9-8 tar_1.30+dfsg-3 tzdata_2018i-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Sep 14 21:03:17 2018 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.1+ds-1.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.15.1+ds dpkg-source: info: unpacking python-pysam_0.15.1+ds.orig.tar.gz dpkg-source: info: unpacking python-pysam_0.15.1+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying skip_test_needing_missing_data.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-15634523 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15634523 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15634523 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 0.15.1+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully find . -name "*.bai*" -delete find . -name "*.cram*" -delete #find . -name "*.bam" -delete # which deletes files tested 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 rm -rf .pytest_cache/ dh clean --with python2,python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.15.1+ds' dh_auto_clean I: pybuild base:217: 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-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.7' 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-0.15.1+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:217: 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:217: python3.7 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:217: /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-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/version.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/config.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/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/libcsamtools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/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-armhf-2.7 creating build/temp.linux-armhf-2.7/pysam arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c building 'pysam.libcsamtools' extension creating build/temp.linux-armhf-2.7/samtools creating build/temp.linux-armhf-2.7/samtools/lz4 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-armhf-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamtools.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c building 'pysam.libcbcftools' extension creating build/temp.linux-armhf-2.7/bcftools arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-armhf-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-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 [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] args->aux.ploidy = (uint8_t*) malloc(args->nsamples); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, 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:539:14: note: in a call to allocation function ‘malloc’ declared here extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur; ^~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcftools.o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcutils.pyx to pysam/libcutils.c building 'pysam.libcutils' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6113:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] bcftools_set_stderr(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stderr pysam/libcutils.c:6285:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] bcftools_set_stdout_fn(__pyx_t_13); ^~~~~~~~~~~~~~~~~~~~~~ samtools_set_stdout_fn pysam/libcutils.c:6296:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] bcftools_set_stdout(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stdout pysam/libcutils.c:7128:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] bcftools_set_optind(1); ^~~~~~~~~~~~~~~~~~~ samtools_set_optind pysam/libcutils.c:7207:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ samtools_main pysam/libcutils.c:7276:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] bcftools_unset_stderr(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stderr pysam/libcutils.c:7312:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] bcftools_unset_stdout(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:11374:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5812:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armhf-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcutils.o build/temp.linux-armhf-2.7/pysam/pysam_util.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c building 'pysam.libcalignmentfile' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:30109:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); ~^~~~~~~~~~~~~~~~~~~ In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:573: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); ~~~~~~~~~~~~~~~~~~~~~~^~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28362:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] (void)(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:13970:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c building 'pysam.libcsamfile' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c building 'pysam.libcalignedsegment' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-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:83, from pysam/libcalignedsegment.c:4: pysam/libcalignedsegment.c: In function ‘initlibcalignedsegment’: /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libcalignedsegment.c:2140:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libcalignedsegment.c:58727:5: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyDict_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libcalignedsegment.c:2140:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libcalignedsegment.c:58743:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14246:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabix.pyx to pysam/libctabix.c building 'pysam.libctabix' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8706:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13977:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 975, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14009:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14379:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) ^~~~~~~~ arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c building 'pysam.libcfaidx' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcf.pyx to pysam/libcbcf.c building 'pysam.libcbcf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:33142:3: 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, from pysam/libcbcf.c:572: /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) ^~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c building 'pysam.libcbgzf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c building 'pysam.libctabixproxies' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-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:83, from pysam/libctabixproxies.c:4: pysam/libctabixproxies.c: In function ‘initlibctabixproxies’: /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19208:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19211:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19238:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19266:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19320:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19323:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19380:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19434:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19437:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19468:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19486:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19504:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19522:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19540:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyFloat_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19558:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19576:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19594:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19612:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19630:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19648:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19666:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19689:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19707:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19725:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19743:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19761:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19779:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19797:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19815:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19833:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/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 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.71’: pysam/libcvcf.c:24714:15: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_9 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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-s7Ya6r/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN I: pybuild base:217: /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-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/version.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/config.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/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/libcsamtools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/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-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/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-armhf-3.7 creating build/temp.linux-armhf-3.7/pysam arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libchtslib.o build/temp.linux-armhf-3.7/pysam/htslib_util.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) building 'pysam.libcsamtools' extension creating build/temp.linux-armhf-3.7/samtools creating build/temp.linux-armhf-3.7/samtools/lz4 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamtools.o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) building 'pysam.libcbcftools' extension creating build/temp.linux-armhf-3.7/bcftools arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcftools.o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcutils.c -o build/temp.linux-armhf-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6113:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] bcftools_set_stderr(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stderr pysam/libcutils.c:6285:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] bcftools_set_stdout_fn(__pyx_t_13); ^~~~~~~~~~~~~~~~~~~~~~ samtools_set_stdout_fn pysam/libcutils.c:6296:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] bcftools_set_stdout(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stdout pysam/libcutils.c:7128:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] bcftools_set_optind(1); ^~~~~~~~~~~~~~~~~~~ samtools_set_optind pysam/libcutils.c:7207:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ samtools_main pysam/libcutils.c:7276:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] bcftools_unset_stderr(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stderr pysam/libcutils.c:7312:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] bcftools_unset_stdout(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:480:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^~~~~~~~~~~~~~~ pysam/libcutils.c:5812:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcutils.o build/temp.linux-armhf-3.7/pysam/pysam_util.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcsamtools.cpython-37m-arm-linux-gnueabihf -lcbcftools.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:30109:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); ~^~~~~~~~~~~~~~~~~~~ In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:573: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); ~~~~~~~~~~~~~~~~~~~~~~^~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28362:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] (void)(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:13970:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignmentfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14246:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libctabix.c -o build/temp.linux-armhf-3.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8706:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13977:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 975, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14009:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14379:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) ^~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabix.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcfaidx.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:33142:3: 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, from pysam/libcbcf.c:572: /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) ^~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbgzf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabixproxies.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.73’: pysam/libcvcf.c:24714:15: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_9 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcvcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-pysam-0.15.1+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view -bS ex2.sam > ex2.bam samtools index ex2.bam samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view -bS with_md.sam > with_md.bam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view -buS ex2.sam > uncompressed.bam samtools view -bS ex9_nofail.sam > ex9_nofail.bam samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam samtools view -bS tag_bug.sam > tag_bug.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam samtools view -bS test_unaligned.sam > test_unaligned.bam samtools view -bS ex10.sam > ex10.bam samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam samtools view -bS example_empty_header.sam > example_empty_header.bam samtools view -bS ex4.sam > ex4.bam samtools view -bS ex9_fail.sam > ex9_fail.bam samtools view -bS issue100.sam > issue100.bam samtools view -bS ex5.sam > ex5.bam samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam samtools view -bS ex6.sam > ex6.bam samtools view -bS rg_with_tab.sam > rg_with_tab.bam samtools view -bS ex_spliced.sam > ex_spliced.bam samtools view -bS example_btag.sam > example_btag.bam samtools view -bS test_query_position.sam > test_query_position.bam touch tmp.list samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam rm -f tmp.list samtools view -bS example_user_header.sam > example_user_header.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS ex3.sam > ex3.bam samtools index ex9_nofail.bam samtools index example_dash_in_chr.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index example_empty_with_header.bam samtools index test_unaligned.bam samtools index ex10.bam samtools index example_aligned_pairs.bam samtools index example_empty_header.bam samtools index ex4.bam samtools index ex9_fail.bam samtools index issue100.bam samtools index ex5.bam samtools index example_reverse_complement.bam samtools index ex6.bam samtools index rg_with_tab.bam samtools index ex_spliced.bam samtools index example_btag.bam samtools index test_query_position.bam samtools index example_unmapped_reads_no_sq.bam samtools index example_user_header.bam samtools index ex8.bam samtools index ex3.bam samtools view -bC -T ex1.fa ex1.sam > ex1.cram samtools view -bC -T ex1.fa ex2.sam > ex2.cram samtools view -bC -T ex1.fa ex3.sam > ex3.cram samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai head -c 124000 ex2.bam > ex2_truncated.bam grep "^@" ex2.sam | samtools view -Sb - > empty.bam samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam rm with_md.sam make[2]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf make[2]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' dh_auto_test I: pybuild base:217: cd /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests ============================= test session starts ============================== platform linux2 -- Python 2.7.15+, pytest-3.10.1, py-1.7.0, pluggy-0.8.0 -- /usr/bin/python2.7 cachedir: .pytest_cache rootdir: /<>/python-pysam-0.15.1+ds, inifile: setup.cfg collecting ... collected 920 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection FAILED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection FAILED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing SKIPPED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) FAILED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =================================== FAILURES =================================== _________ TestSetTagGetTag.test_set_tag_with_automated_type_detection __________ self = def test_set_tag_with_automated_type_detection(self): self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c") self.check_tag('TT', -(1 << 7) - 1, value_type=None, alt_value_type="s") self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s") self.check_tag('TT', -(1 << 15) - 1, value_type=None, alt_value_type="i") > self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i") tests/AlignedSegment_test.py:1184: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignedSegment_test.py:1135: in check_tag a.set_tag(tag, value, value_type=value_type) pysam/libcalignedsegment.pyx:2223: in pysam.libcalignedsegment.AlignedSegment.set_tag ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: can't guess type or invalid type code specified: -2147483648 None pysam/libcalignedsegment.pyx:2302: ValueError _________ TestSetTagsGetTag.test_set_tag_with_automated_type_detection _________ self = def test_set_tag_with_automated_type_detection(self): self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c") self.check_tag('TT', -(1 << 7) - 1, value_type=None, alt_value_type="s") self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s") self.check_tag('TT', -(1 << 15) - 1, value_type=None, alt_value_type="i") > self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i") tests/AlignedSegment_test.py:1184: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignedSegment_test.py:1213: in check_tag a.set_tags([(tag, value, value_type)]) pysam/libcalignedsegment.pyx:2568: in pysam.libcalignedsegment.AlignedSegment.set_tags ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: could not deduce typecode for value -2147483648 pysam/libcalignedsegment.pyx:415: ValueError _____________________ TestSettingRecordValues.testGenotype _____________________ self = def testGenotype(self): with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf: record = next(inf) sample = record.samples["NA00001"] print(sample["GT"]) self.assertEqual(sample["GT"], (0, 0)) > sample["GT"] = sample["GT"] tests/VariantFile_test.py:592: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcbcf.pyx:3442: in pysam.libcbcf.VariantRecordSample.__setitem__ ??? pysam/libcbcf.pyx:855: in pysam.libcbcf.bcf_format_set_value ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E TypeError: invalid value for Integer format pysam/libcbcf.pyx:588: TypeError =============================== warnings summary =============================== .pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: https://docs.pytest.org/en/latest/warnings.html ======== 3 failed, 900 passed, 17 skipped, 1 warnings in 124.17 seconds ======== E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned exit code 13 make[1]: *** [debian/rules:31: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds' make: *** [debian/rules:24: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190101-1135 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 143992 Build-Time: 1258 Distribution: disco-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 56 Job: python-pysam_0.15.1+ds-1.dsc Machine Architecture: arm64 Package: python-pysam Package-Time: 1316 Source-Version: 0.15.1+ds-1 Space: 143992 Status: attempted Version: 0.15.1+ds-1 -------------------------------------------------------------------------------- Finished at 20190101-1135 Build needed 00:21:56, 143992k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=armhf PACKAGEBUILD-15634523 Scanning for processes to kill in build PACKAGEBUILD-15634523