python-pysam →
0.12.0.1+ds-4 →
armhf → 2017-11-26 11:11:39
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| python-pysam 0.12.0.1+ds-4 (armhf) Sun, 26 Nov 2017 10:39:42 +0000 |
+==============================================================================+
Package: python-pysam
Version: 0.12.0.1+ds-4
Source Version: 0.12.0.1+ds-4
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-0f26200e-5503-490b-b330-c4133f44578b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.2 MB]
Fetched 22.6 MB in 8s (2730 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/python-pysam.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/python-pysam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2510 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main python-pysam 0.12.0.1+ds-4 (dsc) [2565 B]
Get:2 http://172.17.0.1/private buster-staging/main python-pysam 0.12.0.1+ds-4 (tar) [2498 kB]
Get:3 http://172.17.0.1/private buster-staging/main python-pysam 0.12.0.1+ds-4 (diff) [9440 B]
Fetched 2510 kB in 0s (6701 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-1P8Gl4/python-pysam-0.12.0.1+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-1P8Gl4' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-ObZGIy/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-ObZGIy/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ObZGIy/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (6281 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 56 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15098 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), dh-exec, dh-python, libhts-dev (>= 1.5-3), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.5), bcftools (>= 1.5), python-pytest, python3-pytest
Filtered Build-Depends: debhelper (>= 10), dh-exec, dh-python, libhts-dev (>= 1.5-3), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.5), bcftools (>= 1.5), python-pytest, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-ObZGIy/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-python-pysam-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Sources [595 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ Packages [663 B]
Fetched 2591 B in 0s (7594 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbsd0 libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1
libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev
libpython3.6-minimal libpython3.6-stdlib librtmp1 libsigsegv2 libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-all python-all-dev python-dev python-minimal python-pkg-resources
python-py python-pytest python-setuptools python2.7 python2.7-dev
python2.7-minimal python3 python3-all python3-all-dev python3-dev
python3-minimal python3-pkg-resources python3-py python3-pytest
python3-setuptools python3.6 python3.6-dev python3.6-minimal samtools tabix
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib
texlive-latex-recommended wamerican | wordlist whois vacation cython-doc
dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc less www-browser libmail-box-perl python-doc python-tk subversion
python-pytest-xdist python-mock python-setuptools-doc python2.7-doc
binfmt-support python3-doc python3-tk python3-venv python3.6-venv
python3.6-doc
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix 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
file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbsd0 libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts2 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1
libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev
libpython3.6-minimal libpython3.6-stdlib librtmp1 libsigsegv2 libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-all python-all-dev python-dev python-minimal python-pkg-resources
python-py python-pytest python-setuptools python2.7 python2.7-dev
python2.7-minimal python3 python3-all python3-all-dev python3-dev
python3-minimal python3-pkg-resources python3-py python3-pytest
python3-setuptools python3.6 python3.6-dev python3.6-minimal samtools
sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
0 upgraded, 93 newly installed, 0 to remove and 56 not upgraded.
Need to get 67.9 MB of archives.
After this operation, 192 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ObZGIy/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-3 [95.9 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-2 [393 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-2 [1091 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-1 [40.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-2 [73.6 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-2 [1854 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-2 [292 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-1 [20.1 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-1 [155 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.3-1 [564 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.3-1 [1232 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.3-2 [35.7 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.3-1 [2055 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.3-1 [218 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.3-2 [19.1 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dh-python all 2.20170125 [86.8 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.3-2 [22.1 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
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Get:27 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.2 [12.1 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5.1 [608 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.2-2 [58.6 kB]
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Get:40 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.2-2 [263 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.2-2 [133 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.27.0-1 [71.0 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.19.1-3 [43.2 kB]
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Get:49 http://172.17.0.1/private buster-staging/main armhf cython armhf 0.26.1-0.4 [1747 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf cython3 armhf 0.26.1-0.4 [1779 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
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Get:53 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
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Get:59 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
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Get:65 http://172.17.0.1/private buster-staging/main armhf tabix armhf 1.5-4 [247 kB]
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Get:67 http://172.17.0.1/private buster-staging/main armhf libpython2.7 armhf 2.7.14-2 [904 kB]
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Get:70 http://172.17.0.1/private buster-staging/main armhf libpython-all-dev armhf 2.7.14-1 [958 B]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpython3.6 armhf 3.6.3-1 [1228 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpython3.6-dev armhf 3.6.3-1 [2252 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpython3-dev armhf 3.6.3-2 [19.2 kB]
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Get:75 http://172.17.0.1/private buster-staging/main armhf python-all armhf 2.7.14-1 [942 B]
Get:76 http://172.17.0.1/private buster-staging/main armhf python2.7-dev armhf 2.7.14-2 [295 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf python-dev armhf 2.7.14-1 [1130 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf python-all-dev armhf 2.7.14-1 [964 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 36.7.1-1 [171 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf python-py all 1.4.34-3 [83.5 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf python-pytest all 3.2.1-2 [200 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf python-setuptools all 36.7.1-1 [305 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf python3-all armhf 3.6.3-2 [1024 B]
Get:84 http://172.17.0.1/private buster-staging/main armhf python3.6-dev armhf 3.6.3-1 [510 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf python3-dev armhf 3.6.3-2 [1236 B]
Get:86 http://172.17.0.1/private buster-staging/main armhf python3-all-dev armhf 3.6.3-2 [1048 B]
Get:87 http://172.17.0.1/private buster-staging/main armhf python3-pkg-resources all 36.7.1-1 [141 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf python3-py all 1.4.34-3 [83.6 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf python3-pytest all 3.2.1-2 [200 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf python3-setuptools all 36.7.1-1 [223 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.5-1 [225 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up bsdmainutils (9.0.14) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
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update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up python (2.7.14-1) ...
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Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-17) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-6+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-12 gcc-7_7.2.0-12 libc6-dev_2.24-17 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha3 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 bcftools_1.5-3 binutils_2.29.1-6+rpi1 binutils-arm-linux-gnueabihf_2.29.1-6+rpi1 binutils-common_2.29.1-6+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-12 cython_0.26.1-0.4 cython3_0.26.1-0.4 dash_0.5.8-2.5 debconf_1.5.64 debhelper_10.10.9 debianutils_4.8.2 dh-autoreconf_15 dh-exec_0.23 dh-python_2.20170125 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.1-5 dmsetup_2:1.02.142-1 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-1 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-12 gcc-7-base_7.2.0-12 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-5 gnupg-agent_2.2.1-5 gnupg-l10n_2.2.1-5 gnupg-utils_2.2.1-5 gpg_2.2.1-5 gpg-agent_2.2.1-5 gpg-wks-client_2.2.1-5 gpg-wks-server_2.2.1-5 gpgconf_2.2.1-5 gpgsm_2.2.1-5 gpgv_2.2.1-5 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.1-2 libapt-pkg5.0_1.6~alpha3 libarchive-zip-perl_1.59-1 libasan4_7.2.0-12 libassuan0_2.4.3-3 libatomic1_7.2.0-12 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-1 libaudit1_1:2.8.1-1 libbinutils_2.29.1-6+rpi1 libblkid1_2.30.2-0.1 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-17 libc-dev-bin_2.24-17 libc6_2.24-17 libc6-dev_2.24-17 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-12 libcilkrts5_7.2.0-12 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.56.1-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.22-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.19.0.4 libdrm-common_2.4.84-2+rpi1 libdrm2_2.4.84-2+rpi1 libexpat1_2.2.3-2 libexpat1-dev_2.2.3-2 libfakeroot_1.22-1 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-12 libgcc1_1:7.2.0-12 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-12 libgpg-error0_1.27-4 libgssapi-krb5-2_1.15.2-2 libhogweed4_3.3-2 libhts-dev_1.5-4 libhts2_1.5-4 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libk5crypto3_1.15.2-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.2-2 libkrb5support0_1.15.2-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpdec2_2.4.2-1 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnghttp2-14_1.27.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.1-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.19.1-3 libpython-all-dev_2.7.14-1 libpython-dev_2.7.14-1 libpython-stdlib_2.7.14-1 libpython2.7_2.7.14-2 libpython2.7-dev_2.7.14-2 libpython2.7-minimal_2.7.14-2 libpython2.7-stdlib_2.7.14-2 libpython3-all-dev_3.6.3-2 libpython3-dev_3.6.3-2 libpython3-stdlib_3.6.3-2 libpython3.6_3.6.3-1 libpython3.6-dev_3.6.3-1 libpython3.6-minimal_3.6.3-1 libpython3.6-stdlib_3.6.3-1 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.20.1-2 libss2_1.43.7-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 libsystemd0_235-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-12 libudev1_235-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5.1 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.30.2-0.1 mountall_2.54 multiarch-support_2.24-17 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.14-1 python-all_2.7.14-1 python-all-dev_2.7.14-1 python-dev_2.7.14-1 python-minimal_2.7.14-1 python-pkg-resources_36.7.1-1 python-py_1.4.34-3 python-pytest_3.2.1-2 python-setuptools_36.7.1-1 python2.7_2.7.14-2 python2.7-dev_2.7.14-2 python2.7-minimal_2.7.14-2 python3_3.6.3-2 python3-all_3.6.3-2 python3-all-dev_3.6.3-2 python3-dev_3.6.3-2 python3-minimal_3.6.3-2 python3-pkg-resources_36.7.1-1 python3-py_1.4.34-3 python3-pytest_3.2.1-2 python3-setuptools_36.7.1-1 python3.6_3.6.3-1 python3.6-dev_3.6.3-1 python3.6-minimal_3.6.3-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 samtools_1.5-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_235-2 sysvinit-utils_2.88dsf-59.10 tabix_1.5-4 tar_1.29b-2 tzdata_2017c-1 udev_235-2 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Nov 10 19:15:13 2017 UTC
gpgv: using RSA key 8B7868786C33E5C64C4D0A480816B9E18C762BAD
gpgv: issuer "mattia@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.12.0.1+ds-4.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.12.0.1+ds
dpkg-source: info: unpacking python-pysam_0.12.0.1+ds.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.12.0.1+ds-4.debian.tar.xz
dpkg-source: info: applying execute-linking-tests-only-when-explicitely-reque.patch
dpkg-source: info: applying rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
dpkg-source: info: applying xfail.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-0f26200e-5503-490b-b330-c4133f44578b
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.12.0.1+ds-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build python-pysam-0.12.0.1+ds
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf tests/pysam_test_work \
tests/example_htslib.gtf.gz.tbi \
tests/log.txt \
tests/test.bam \
tests/_compile_test.c \
tests/pysam_ex2.sam \
tests/__pycache__ \
pysam/calignmentfile.c \
pysam/cbcf.c \
tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
tests/pysam_data/ex1.fa.gz \
tests/pysam_data/ex1.fa.gz.gzi \
tests/pysam_data/ex1_csi.bam.csi
dh clean --with python2,python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds'
dh_auto_clean
I: pybuild base:184: python2.7 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/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:184: python3.6 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.6' does not exist -- can't clean it
rm -f \
pysam/config.py \
pysam/config.h \
pysam/lib*.c \
samtools/config.h \
bcftools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds'
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python2,python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:184: python3.6 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libchtslib.c:4:
pysam/libchtslib.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libchtslib.c:1627:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-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,-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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+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/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libcsamfile.c:4:
pysam/libcsamfile.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcsamfile.c:1946:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_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,-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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libcalignmentfile.c:4:
pysam/libcalignmentfile.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcalignmentfile.c:2343:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:24737:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
__pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
^
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:23162:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:8785:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_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,-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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-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:78:0,
from pysam/libcalignedsegment.c:4:
pysam/libcalignedsegment.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcalignedsegment.c:2814:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_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,-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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabix.pyx to pysam/libctabix.c
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libctabix.c:4:
pysam/libctabix.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libctabix.c:2270:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8168:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
__pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_2tabix_index’:
pysam/libctabix.c:13112:39: warning: overflow in implicit constant conversion [-Woverflow]
__pyx_t_8 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 918, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:13144:39: warning: overflow in implicit constant conversion [-Woverflow]
__pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 919, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:13446:43: warning: overflow in implicit constant conversion [-Woverflow]
__pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 943, __pyx_L1_error)
^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armhf-2.7/pysam/tabix_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,-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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o build/temp.linux-armhf-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-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:78:0,
from pysam/libctabixproxies.c:4:
pysam/libctabixproxies.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libctabixproxies.c:1639:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libcvcf.c:4:
pysam/libcvcf.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcvcf.c:2203:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.69’:
pysam/libcvcf.c:24706:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
__pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libcbcf.c:4:
pysam/libcbcf.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcbcf.c:2716:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:32796:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
__pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5:0,
from pysam/libcbcf.c:489:
/usr/include/htslib/vcf.h:439:11: note: declared here
char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libcbgzf.c:4:
pysam/libcbgzf.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcbgzf.c:1206:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libcfaidx.c:4:
pysam/libcfaidx.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcfaidx.c:1684:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-2.7/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-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 -shared -Wl,-O1 -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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+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_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam.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/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-2.7/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-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/arm-linux-gnueabihf/bits/string2.h:319:0,
from /usr/include/string.h:630,
from bcftools/vcfcall.c.pysam.c:28:
bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’:
/usr/include/stdlib.h:427:14: 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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-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=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-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 -shared -Wl,-O1 -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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+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/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.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/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.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/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcutils.pyx to pysam/libcutils.c
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
from pysam/libcutils.c:4:
pysam/libcutils.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
pysam/libcutils.c:1369:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:10757:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return PyInt_FromLong((long) value);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:5606:7: note: ‘__pyx_v_retval’ was declared here
int __pyx_v_retval;
^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-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,-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-LSpDd8/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+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 -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN
I: pybuild base:184: /usr/bin/python3 setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.6
creating build/temp.linux-armhf-3.6/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libchtslib.o build/temp.linux-armhf-3.6/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.cpython-36m-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 -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.6/pysam/libcsamfile.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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/pysam/htslib_util.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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.6/pysam/samfile_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcsamfile.o build/temp.linux-armhf-3.6/pysam/htslib_util.o build/temp.linux-armhf-3.6/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.cpython-36m-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 -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.6/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:24737:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
__pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
^
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:23162:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:8785:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/pysam/htslib_util.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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.6/pysam/samfile_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignmentfile.o build/temp.linux-armhf-3.6/pysam/htslib_util.o build/temp.linux-armhf-3.6/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.cpython-36m-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 -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.6/pysam/libcalignedsegment.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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/pysam/htslib_util.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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.6/pysam/samfile_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignedsegment.o build/temp.linux-armhf-3.6/pysam/htslib_util.o build/temp.linux-armhf-3.6/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.cpython-36m-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 -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libctabix.c -o build/temp.linux-armhf-3.6/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8168:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
__pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_2tabix_index’:
pysam/libctabix.c:13112:39: warning: overflow in implicit constant conversion [-Woverflow]
__pyx_t_8 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 918, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:13144:39: warning: overflow in implicit constant conversion [-Woverflow]
__pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 919, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:13446:43: warning: overflow in implicit constant conversion [-Woverflow]
__pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 943, __pyx_L1_error)
^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/tabix_util.c -o build/temp.linux-armhf-3.6/pysam/tabix_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libctabix.o build/temp.linux-armhf-3.6/pysam/tabix_util.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.cpython-36m-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 -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.6/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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.6/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.71’:
pysam/libcvcf.c:24706:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
__pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.6/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:32796:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
__pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5:0,
from pysam/libcbcf.c:489:
/usr/include/htslib/vcf.h:439:11: note: declared here
char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.6/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbgzf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.6/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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcfaidx.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.cpython-36m-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-3.6/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_index.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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcsamtools.o build/temp.linux-armhf-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.6/samtools/padding.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.6/samtools/dict.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats.c.pysam.o build/temp.linux-armhf-3.6/samtools/sample.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.6/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.6/samtools/phase.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.6/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_index.c.pysam.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamtools.cpython-36m-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-3.6/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfmerge.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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.6/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 -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.6/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/hclust.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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbcftools.o build/temp.linux-armhf-3.6/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.6/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.6/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.6/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.6/bcftools/main.c.pysam.o build/temp.linux-armhf-3.6/bcftools/em.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.6/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.6/bcftools/version.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.6/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.6/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.6/bcftools/hclust.c.pysam.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcftools.cpython-36m-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 -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcutils.c -o build/temp.linux-armhf-3.6/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:304:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^~~~~~~~~~~~~~~
pysam/libcutils.c:5606:7: note: ‘__pyx_v_retval’ was declared here
int __pyx_v_retval;
^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.6/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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.12.0.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcutils.o build/temp.linux-armhf-3.6/pysam/pysam_util.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcsamtools.cpython-36m-arm-linux-gnueabihf -lcbcftools.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.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 tag_bug.sam > tag_bug.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 test_unaligned.sam > test_unaligned.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS issue100.sam > issue100.bam
samtools view -bS ex5.sam > ex5.bam
samtools view -bS ex6.sam > ex6.bam
samtools view -bS rg_with_tab.sam > rg_with_tab.bam
samtools view -bS ex_spliced.sam > ex_spliced.bam
samtools view -bS example_btag.sam > example_btag.bam
samtools view -bS test_query_position.sam > test_query_position.bam
touch tmp.list
samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam
rm -f tmp.list
samtools view -bS ex4.sam > ex4.bam
samtools view -bS example_user_header.sam > example_user_header.bam
samtools view -bS ex8.sam > ex8.bam
samtools view -bS ex3.sam > ex3.bam
samtools index ex9_nofail.bam
samtools index test_mapped_unmapped.bam
samtools index softclip.bam
samtools index example_empty_with_header.bam
samtools index tag_bug.bam
samtools index ex10.bam
samtools index example_aligned_pairs.bam
samtools index example_empty_header.bam
samtools index test_unaligned.bam
samtools index ex9_fail.bam
samtools index issue100.bam
samtools index ex5.bam
samtools index ex6.bam
samtools index rg_with_tab.bam
samtools index ex_spliced.bam
samtools index example_btag.bam
samtools index test_query_position.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index ex4.bam
samtools index example_user_header.bam
samtools index ex8.bam
samtools index ex3.bam
samtools view -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/cbcf_data'
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz # create csi index
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -p vcf example_vcf40.vcf.gz # create tbi index
bcftools index example_vcf40.vcf.gz # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf missing_genotypes.vcf.gz # create tbi index
bcftools index missing_genotypes.vcf.gz # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -p vcf example_vcf42.vcf.gz # create tbi index
bcftools index example_vcf42.vcf.gz # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index
bcftools index example_vcf42_only_header.vcf.gz # create csi index
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.bcf
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf42_only_header.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:184: cd /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m pytest tests
============================= test session starts ==============================
platform linux2 -- Python 2.7.14, pytest-3.2.1, py-1.4.34, pluggy-0.4.0 -- /usr/bin/python2.7
cachedir: ../../../.cache
rootdir: /<<BUILDDIR>>/python-pysam-0.12.0.1+ds, inifile: setup.cfg
collecting ... In file included from /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c:490:0:
/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
int hts_get_verbosity();
^~~
In file included from /usr/include/python2.7/Python.h:78:0,
from /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c:4:
/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
: malloc((n) ? (n) : 1))
^
/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/_compile_test.c:2089:28: note: in expansion of macro ‘PyMem_NEW’
op->data.ob_item = PyMem_NEW(char, nbytes);
^~~~~~~~~
collected 779 items
tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestAsString::testAsString PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
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tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED
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tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM <- ../../../usr/lib/python2.7/unittest/case.py PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFile_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFile_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFile_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestTagParsing::testArrayTags PASSED
tests/AlignmentFile_test.py::TestTagParsing::testCigar PASSED
tests/AlignmentFile_test.py::TestTagParsing::testCigarString PASSED
tests/AlignmentFile_test.py::TestTagParsing::testLongTags PASSED
tests/AlignmentFile_test.py::TestTagParsing::testNegativeIntegers PASSED
tests/AlignmentFile_test.py::TestTagParsing::testNegativeIntegers2 PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestHeaderSAM::testHeaders PASSED
tests/AlignmentFile_test.py::TestHeaderSAM::testNameMapping PASSED
tests/AlignmentFile_test.py::TestHeaderBAM::testHeaders PASSED
tests/AlignmentFile_test.py::TestHeaderBAM::testNameMapping PASSED
tests/AlignmentFile_test.py::TestHeaderCRAM::testHeaders PASSED
tests/AlignmentFile_test.py::TestHeaderCRAM::testNameMapping PASSED
tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED
tests/AlignmentFile_test.py::TestHeaderWriteRead::test_BAM PASSED
tests/AlignmentFile_test.py::TestHeaderWriteRead::test_CRAM PASSED
tests/AlignmentFile_test.py::TestHeaderWriteRead::test_SAM PASSED
tests/AlignmentFile_test.py::TestUnmappedReads::testBAM PASSED
tests/AlignmentFile_test.py::TestPileupObjects::testIteratorOutOfScope PASSED
tests/AlignmentFile_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFile_test.py::TestPileupObjects::testPileupRead PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
[E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegion PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegion PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegion PASSED
tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestPileup::testAllStepper PASSED
tests/AlignmentFile_test.py::TestPileup::testSamtoolsStepper PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz
PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo PASSED
tests/VariantFile_test.py::TestParsing::testPos PASSED
tests/VariantFile_test.py::TestParsing::testQual PASSED
tests/VariantFile_test.py::TestParsing::testRef PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
tests/VariantFile_test.py::TestParsing::testStart PASSED
tests/VariantFile_test.py::TestParsing::testStop PASSED
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
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::TestSubsetting::testSubsetting PASSED
tests/compile_test.py::BAMTest::testCount PASSED
tests/compile_test.py::GTFTest::testCount PASSED
tests/faidx_test.py::TestFastaFile::testFetch PASSED
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
tests/faidx_test.py::TestFastaFile::testLength PASSED
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
tests/faidx_test.py::TestFastaFilePathIndex::testGarbageIndex PASSED
tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithOtherIndex PASSED
tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithStandardIndex PASSED
tests/faidx_test.py::TestFastaFilePathIndex::testOpenWithoutIndex PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::testGarbageIndex PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithOtherIndex PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithStandardIndex PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::testOpenWithoutIndex PASSED
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
tests/samtools_test.py::SamtoolsTest::testStatements PASSED
tests/samtools_test.py::SamtoolsTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
tests/samtools_test.py::PysamTest::testStatements PASSED
tests/samtools_test.py::PysamTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] PL should be declared as Number=G
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_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::VCFFromVCFTest_vcf_v42::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED
tests/tabix_test.py::TestCompression::testCompression PASSED
tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionSam::testCompression PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionBed::testCompression PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testCompression PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestGZFile::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED
tests/tabix_test.py::TestIterationWithComments::testAll PASSED
tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithComments::testReopening PASSED
tests/tabix_test.py::TestIterators::testClosedFile PASSED
tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED
tests/tabix_test.py::TestIterators::testIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED
tests/tabix_test.py::TestBed::testRead PASSED
tests/tabix_test.py::TestBed::testWrite PASSED
tests/tabix_test.py::TestVCFFromTabix::testRead PASSED
tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED
tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/tabix_test.py::TestRemoteFileHTTP::testHeader PASSED
tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED
tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED
tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testScope PASSED
tests/tabix_test.py::TestContextManager::testManager PASSED
tests/tabixproxies_test.py::TestParser::testCopy PASSED
tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestParser::testRead PASSED
tests/tabixproxies_test.py::TestParser::testUnset PASSED
tests/tabixproxies_test.py::TestParser::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::testCopy PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGTF::testRead PASSED
tests/tabixproxies_test.py::TestGTF::testSetting PASSED
tests/tabixproxies_test.py::TestGTF::testUnset PASSED
tests/tabixproxies_test.py::TestGTF::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::testCopy PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testRead PASSED
tests/tabixproxies_test.py::TestGFF3::testSetting PASSED
tests/tabixproxies_test.py::TestGFF3::testUnset PASSED
tests/tabixproxies_test.py::TestGFF3::testWrite PASSED
tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED
tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED
tests/test_samtools_python.py::test_bedcov_split_lines PASSED
tests/test_samtools_python.py::test_idxstats_parse PASSED
tests/test_samtools_python.py::test_bedcov PASSED
=================================== FAILURES ===================================
_____________________ TestSettingRecordValues.testGenotype _____________________
self = <VariantFile_test.TestSettingRecordValues testMethod=testGenotype>
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:490:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcbcf.pyx:3423: in pysam.libcbcf.VariantRecordSample.__setitem__
???
pysam/libcbcf.pyx:854: in pysam.libcbcf.bcf_format_set_value
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: invalid value for Integer format
pysam/libcbcf.pyx:587: TypeError
=============================== warnings summary ===============================
.pybuild/pythonX.Y_2.7/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2
/<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build/tests/AlignmentFile_test.py:1865: UserWarning: no BGZF EOF marker; file may be truncated
ignore_truncation=True)
-- Docs: http://doc.pytest.org/en/latest/warnings.html
======== 1 failed, 768 passed, 10 skipped, 1 warnings in 203.82 seconds ========
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/python-pysam-0.12.0.1+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m pytest tests
dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned exit code 13
debian/rules:27: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.12.0.1+ds'
debian/rules:20: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-11-26T11:11:37Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 125072
Build-Time: 1490
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 408
Job: python-pysam_0.12.0.1+ds-4
Machine Architecture: armhf
Package: python-pysam
Package-Time: 1915
Source-Version: 0.12.0.1+ds-4
Space: 125072
Status: attempted
Version: 0.12.0.1+ds-4
--------------------------------------------------------------------------------
Finished at 2017-11-26T11:11:37Z
Build needed 00:31:55, 125072k disk space