Thu Sep 2 13:02:28 UTC 2021 I: starting to build python-pysam/buster/armhf on jenkins on '2021-09-02 13:02'
Thu Sep 2 13:02:28 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_2/2093/console.log
Thu Sep 2 13:02:28 UTC 2021 I: Downloading source for buster/python-pysam=0.15.2+ds-2
--2021-09-02 13:02:28-- http://deb.debian.org/debian/pool/main/p/python-pysam/python-pysam_0.15.2%2bds-2.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2528 (2.5K)
Saving to: ‘python-pysam_0.15.2+ds-2.dsc’
0K .. 100% 169M=0s
2021-09-02 13:02:28 (169 MB/s) - ‘python-pysam_0.15.2+ds-2.dsc’ saved [2528/2528]
Thu Sep 2 13:02:28 UTC 2021 I: python-pysam_0.15.2+ds-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: python-pysam
Binary: python-pysam, python3-pysam, python-pysam-tests
Architecture: any all
Version: 0.15.2+ds-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>,
Homepage: http://pysam.readthedocs.org/en/latest
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
Testsuite: autopkgtest, autopkgtest-pkg-python
Testsuite-Triggers: @builddeps@
Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix <!nocheck>, samtools (>= 1.9) <!nocheck>, bcftools (>= 1.9) <!nocheck>, python-pytest <!nocheck>, python3-pytest <!nocheck>
Package-List:
python-pysam deb python optional arch=any
python-pysam-tests deb python optional arch=all
python3-pysam deb python optional arch=any
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Files:
89b2c49dd30dbe648036ca7e86103a8e 1370660 python-pysam_0.15.2+ds.orig.tar.xz
106e19251b96d332b4f9207123712c44 11716 python-pysam_0.15.2+ds-2.debian.tar.xz
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Thu Sep 2 13:02:28 UTC 2021 I: Checking whether the package is not for us
Thu Sep 2 13:02:28 UTC 2021 I: Starting 1st build on remote node cbxi4b-armhf-rb.debian.net.
Thu Sep 2 13:02:28 UTC 2021 I: Preparing to do remote build '1' on cbxi4b-armhf-rb.debian.net.
Thu Sep 2 14:58:10 UTC 2021 I: Deleting $TMPDIR on cbxi4b-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Sep 2 01:02:38 -12 2021
I: pbuilder-time-stamp: 1630587758
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz]
I: copying local configuration
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [python-pysam_0.15.2+ds-2.dsc]
I: copying [./python-pysam_0.15.2+ds.orig.tar.xz]
I: copying [./python-pysam_0.15.2+ds-2.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Feb 19 22:46:46 2019 -12
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.2+ds-2.dsc
dpkg-source: info: extracting python-pysam in python-pysam-0.15.2+ds
dpkg-source: info: unpacking python-pysam_0.15.2+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.15.2+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip_test_remote.patch
dpkg-source: info: applying skip_test_needing_missing_data.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying test_index_not_compression
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/28455/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3'
DISTRIBUTION=''
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='8635aa2435d74645aa4e88dd156e1aee'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='28455'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.tQej7znwPx/pbuilderrc_MqoL --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.tQej7znwPx/b1 --logfile b1/build.log python-pysam_0.15.2+ds-2.dsc'
SUDO_GID='116'
SUDO_UID='112'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:8000/'
I: uname -a
Linux cbxi4b 5.10.0-8-armmp #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux
I: ls -l /bin
total 3328
-rwxr-xr-x 1 root root 767656 Apr 17 2019 bash
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2
-rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore
-rwxr-xr-x 1 root root 22432 Feb 28 2019 cat
-rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp
-rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod
-rwxr-xr-x 1 root root 42972 Feb 28 2019 chown
-rwxr-xr-x 1 root root 88376 Feb 28 2019 cp
-rwxr-xr-x 1 root root 75516 Jan 17 2019 dash
-rwxr-xr-x 1 root root 71648 Feb 28 2019 date
-rwxr-xr-x 1 root root 51212 Feb 28 2019 dd
-rwxr-xr-x 1 root root 55672 Feb 28 2019 df
-rwxr-xr-x 1 root root 88444 Feb 28 2019 dir
-rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg
lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname
-rwxr-xr-x 1 root root 22364 Feb 28 2019 echo
-rwxr-xr-x 1 root root 28 Jan 7 2019 egrep
-rwxr-xr-x 1 root root 18260 Feb 28 2019 false
-rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep
-rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt
-rwsr-xr-x 1 root root 21980 Apr 22 2020 fusermount
-rwxr-xr-x 1 root root 124508 Jan 7 2019 grep
-rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip
-rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe
-rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip
-rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname
-rwxr-xr-x 1 root root 43044 Feb 28 2019 ln
-rwxr-xr-x 1 root root 34932 Jul 26 2018 login
-rwxr-xr-x 1 root root 88444 Feb 28 2019 ls
-rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk
-rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir
-rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod
-rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp
-rwxr-xr-x 1 root root 26024 Jan 9 2019 more
-rwsr-xr-x 1 root root 34268 Jan 9 2019 mount
-rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint
-rwxr-xr-x 1 root root 84284 Feb 28 2019 mv
lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd
lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash
-rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink
-rwxr-xr-x 1 root root 42968 Feb 28 2019 rm
-rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir
-rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts
-rwxr-xr-x 1 root root 76012 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Aug 6 20:26 sh -> dash
-rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep
-rwxr-xr-x 1 root root 51124 Feb 28 2019 stty
-rwsr-xr-x 1 root root 42472 Jan 9 2019 su
-rwxr-xr-x 1 root root 22392 Feb 28 2019 sync
-rwxr-xr-x 1 root root 283324 Apr 23 2019 tar
-rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile
-rwxr-xr-x 1 root root 63464 Feb 28 2019 touch
-rwxr-xr-x 1 root root 18260 Feb 28 2019 true
-rwxr-xr-x 1 root root 9636 Apr 22 2020 ulockmgr_server
-rwsr-xr-x 1 root root 21976 Jan 9 2019 umount
-rwxr-xr-x 1 root root 22380 Feb 28 2019 uname
-rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress
-rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir
-rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl
-rwxr-xr-x 1 root root 946 Jan 21 2019 which
lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat
-rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp
-rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff
-rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep
-rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep
-rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce
-rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep
-rwxr-xr-x 1 root root 2205 Jan 5 2019 zless
-rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore
-rwxr-xr-x 1 root root 4552 Jan 5 2019 znew
I: user script /srv/workspace/pbuilder/28455/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 18932 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however:
Package debhelper is not installed.
pbuilder-satisfydepends-dummy depends on dh-exec; however:
Package dh-exec is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.9); however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on python-all-dev; however:
Package python-all-dev is not installed.
pbuilder-satisfydepends-dummy depends on python-setuptools; however:
Package python-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on cython (>= 0.23); however:
Package cython is not installed.
pbuilder-satisfydepends-dummy depends on python3-all-dev; however:
Package python3-all-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on cython3 (>= 0.23); however:
Package cython3 is not installed.
pbuilder-satisfydepends-dummy depends on tabix; however:
Package tabix is not installed.
pbuilder-satisfydepends-dummy depends on samtools (>= 1.9); however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on bcftools (>= 1.9); however:
Package bcftools is not installed.
pbuilder-satisfydepends-dummy depends on python-pytest; however:
Package python-pytest is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest; however:
Package python3-pytest is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bsdmainutils{a} cython{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-all-dev{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.7{a} libpython3.7-dev{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-all{a} python-all-dev{a} python-atomicwrites{a} python-attr{a} python-dev{a} python-funcsigs{a} python-minimal{a} python-more-itertools{a} python-pathlib2{a} python-pkg-resources{a} python-pluggy{a} python-py{a} python-pytest{a} python-scandir{a} python-setuptools{a} python-six{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-all{a} python3-all-dev{a} python3-atomicwrites{a} python3-attr{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pytest{a} python3-setuptools{a} python3-six{a} python3.7{a} python3.7-dev{a} python3.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tabix{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl cwltool krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs
0 packages upgraded, 124 newly installed, 0 to remove and 0 not upgraded.
Need to get 122 MB of archives. After unpacking 258 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2+deb10u1 [104 kB]
Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB]
Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3+deb10u1 [828 kB]
Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB]
Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB]
Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB]
Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB]
Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB]
Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB]
Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u6 [1299 kB]
Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB]
Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB]
Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB]
Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB]
Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB]
Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB]
Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB]
Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB]
Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB]
Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB]
Get: 22 http://deb.debian.org/debian buster/main armhf libpython3.7-minimal armhf 3.7.3-2+deb10u3 [582 kB]
Get: 23 http://deb.debian.org/debian buster/main armhf python3.7-minimal armhf 3.7.3-2+deb10u3 [1466 kB]
Get: 24 http://deb.debian.org/debian buster/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB]
Get: 25 http://deb.debian.org/debian buster/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB]
Get: 26 http://deb.debian.org/debian buster/main armhf libpython3.7-stdlib armhf 3.7.3-2+deb10u3 [1660 kB]
Get: 27 http://deb.debian.org/debian buster/main armhf python3.7 armhf 3.7.3-2+deb10u3 [330 kB]
Get: 28 http://deb.debian.org/debian buster/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB]
Get: 29 http://deb.debian.org/debian buster/main armhf python3 armhf 3.7.3-1 [61.5 kB]
Get: 30 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get: 31 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u2 [242 kB]
Get: 32 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u2 [110 kB]
Get: 33 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u2 [65.6 kB]
Get: 34 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB]
Get: 35 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB]
Get: 36 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB]
Get: 37 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB]
Get: 38 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get: 39 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB]
Get: 40 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get: 41 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB]
Get: 42 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3+deb10u1 [62.3 kB]
Get: 43 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3+deb10u1 [119 kB]
Get: 44 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3+deb10u1 [323 kB]
Get: 45 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3+deb10u1 [137 kB]
Get: 46 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB]
Get: 47 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB]
Get: 48 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB]
Get: 49 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u6 [202 kB]
Get: 50 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB]
Get: 51 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB]
Get: 52 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB]
Get: 53 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB]
Get: 54 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u2 [296 kB]
Get: 55 http://deb.debian.org/debian buster/main armhf libdeflate0 armhf 1.2-1 [46.4 kB]
Get: 56 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB]
Get: 57 http://deb.debian.org/debian buster/main armhf bcftools armhf 1.9-1 [466 kB]
Get: 58 http://deb.debian.org/debian buster/main armhf cython armhf 0.29.2-2 [1306 kB]
Get: 59 http://deb.debian.org/debian buster/main armhf cython3 armhf 0.29.2-2 [1330 kB]
Get: 60 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB]
Get: 61 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB]
Get: 62 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get: 63 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get: 64 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get: 65 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get: 66 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB]
Get: 67 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u3 [1102 kB]
Get: 68 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB]
Get: 69 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+deb10u2 [597 kB]
Get: 70 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB]
Get: 71 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB]
Get: 72 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB]
Get: 73 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 74 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB]
Get: 75 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB]
Get: 76 http://deb.debian.org/debian buster/main armhf dh-exec armhf 0.23.1 [24.9 kB]
Get: 77 http://deb.debian.org/debian buster/main armhf python3-lib2to3 all 3.7.3-1 [76.7 kB]
Get: 78 http://deb.debian.org/debian buster/main armhf python3-distutils all 3.7.3-1 [142 kB]
Get: 79 http://deb.debian.org/debian buster/main armhf dh-python all 3.20190308 [99.3 kB]
Get: 80 http://deb.debian.org/debian buster/main armhf libexpat1-dev armhf 2.2.6-2+deb10u1 [126 kB]
Get: 81 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB]
Get: 82 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB]
Get: 83 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB]
Get: 84 http://deb.debian.org/debian buster/main armhf libpython2.7 armhf 2.7.16-2+deb10u1 [892 kB]
Get: 85 http://deb.debian.org/debian buster/main armhf libpython2.7-dev armhf 2.7.16-2+deb10u1 [31.0 MB]
Get: 86 http://deb.debian.org/debian buster/main armhf libpython2-dev armhf 2.7.16-1 [20.9 kB]
Get: 87 http://deb.debian.org/debian buster/main armhf libpython-dev armhf 2.7.16-1 [20.9 kB]
Get: 88 http://deb.debian.org/debian buster/main armhf libpython-all-dev armhf 2.7.16-1 [1064 B]
Get: 89 http://deb.debian.org/debian buster/main armhf libpython3.7 armhf 3.7.3-2+deb10u3 [1281 kB]
Get: 90 http://deb.debian.org/debian buster/main armhf libpython3.7-dev armhf 3.7.3-2+deb10u3 [47.2 MB]
Get: 91 http://deb.debian.org/debian buster/main armhf libpython3-dev armhf 3.7.3-1 [20.1 kB]
Get: 92 http://deb.debian.org/debian buster/main armhf libpython3-all-dev armhf 3.7.3-1 [1068 B]
Get: 93 http://deb.debian.org/debian buster/main armhf python-all armhf 2.7.16-1 [1044 B]
Get: 94 http://deb.debian.org/debian buster/main armhf python2.7-dev armhf 2.7.16-2+deb10u1 [291 kB]
Get: 95 http://deb.debian.org/debian buster/main armhf python2-dev armhf 2.7.16-1 [1216 B]
Get: 96 http://deb.debian.org/debian buster/main armhf python-dev armhf 2.7.16-1 [1192 B]
Get: 97 http://deb.debian.org/debian buster/main armhf python-all-dev armhf 2.7.16-1 [1068 B]
Get: 98 http://deb.debian.org/debian buster/main armhf python-atomicwrites all 1.1.5-2 [6808 B]
Get: 99 http://deb.debian.org/debian buster/main armhf python-attr all 18.2.0-1 [37.2 kB]
Get: 100 http://deb.debian.org/debian buster/main armhf python-funcsigs all 1.0.2-4 [13.7 kB]
Get: 101 http://deb.debian.org/debian buster/main armhf python-six all 1.12.0-1 [15.7 kB]
Get: 102 http://deb.debian.org/debian buster/main armhf python-more-itertools all 4.2.0-1 [42.3 kB]
Get: 103 http://deb.debian.org/debian buster/main armhf python-scandir armhf 1.9.0-2 [17.0 kB]
Get: 104 http://deb.debian.org/debian buster/main armhf python-pathlib2 all 2.3.3-1 [18.3 kB]
Get: 105 http://deb.debian.org/debian buster/main armhf python-pkg-resources all 40.8.0-1 [182 kB]
Get: 106 http://deb.debian.org/debian buster/main armhf python-pluggy all 0.8.0-1 [20.5 kB]
Get: 107 http://deb.debian.org/debian buster/main armhf python-py all 1.7.0-2 [86.5 kB]
Get: 108 http://deb.debian.org/debian buster/main armhf python-pytest all 3.10.1-2 [243 kB]
Get: 109 http://deb.debian.org/debian buster/main armhf python-setuptools all 40.8.0-1 [382 kB]
Get: 110 http://deb.debian.org/debian buster/main armhf python3-all armhf 3.7.3-1 [1068 B]
Get: 111 http://deb.debian.org/debian buster/main armhf python3.7-dev armhf 3.7.3-2+deb10u3 [509 kB]
Get: 112 http://deb.debian.org/debian buster/main armhf python3-dev armhf 3.7.3-1 [1264 B]
Get: 113 http://deb.debian.org/debian buster/main armhf python3-all-dev armhf 3.7.3-1 [1064 B]
Get: 114 http://deb.debian.org/debian buster/main armhf python3-atomicwrites all 1.1.5-2 [6892 B]
Get: 115 http://deb.debian.org/debian buster/main armhf python3-attr all 18.2.0-1 [37.3 kB]
Get: 116 http://deb.debian.org/debian buster/main armhf python3-six all 1.12.0-1 [15.7 kB]
Get: 117 http://deb.debian.org/debian buster/main armhf python3-more-itertools all 4.2.0-1 [42.2 kB]
Get: 118 http://deb.debian.org/debian buster/main armhf python3-pkg-resources all 40.8.0-1 [153 kB]
Get: 119 http://deb.debian.org/debian buster/main armhf python3-pluggy all 0.8.0-1 [20.6 kB]
Get: 120 http://deb.debian.org/debian buster/main armhf python3-py all 1.7.0-2 [86.6 kB]
Get: 121 http://deb.debian.org/debian buster/main armhf python3-pytest all 3.10.1-2 [243 kB]
Get: 122 http://deb.debian.org/debian buster/main armhf python3-setuptools all 40.8.0-1 [306 kB]
Get: 123 http://deb.debian.org/debian buster/main armhf samtools armhf 1.9-4 [410 kB]
Get: 124 http://deb.debian.org/debian buster/main armhf tabix armhf 1.9-11 [263 kB]
Fetched 122 MB in 13s (9205 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libbsd0:armhf (0.9.1-2+deb10u1) ...
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Unpacking bsdmainutils (11.1.2+b1) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.6-3) ...
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Unpacking groff-base (1.22.4-3+deb10u1) ...
Selecting previously unselected package libpipeline1:armhf.
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Unpacking libpipeline1:armhf (1.5.1-2) ...
Selecting previously unselected package man-db.
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Unpacking man-db (2.8.5-2) ...
Selecting previously unselected package libpython2.7-minimal:armhf.
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Unpacking libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_armhf.deb ...
Unpacking python2.7-minimal (2.7.16-2+deb10u1) ...
Selecting previously unselected package python2-minimal.
Preparing to unpack .../08-python2-minimal_2.7.16-1_armhf.deb ...
Unpacking python2-minimal (2.7.16-1) ...
Selecting previously unselected package python-minimal.
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Unpacking python-minimal (2.7.16-1) ...
Selecting previously unselected package libssl1.1:armhf.
Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u6_armhf.deb ...
Unpacking libssl1.1:armhf (1.1.1d-0+deb10u6) ...
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Unpacking mime-support (3.62) ...
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Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ...
Selecting previously unselected package readline-common.
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Unpacking readline-common (7.0-5) ...
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Unpacking libreadline7:armhf (7.0-5) ...
Selecting previously unselected package libpython2.7-stdlib:armhf.
Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_armhf.deb ...
Unpacking libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_armhf.deb ...
Unpacking python2.7 (2.7.16-2+deb10u1) ...
Selecting previously unselected package libpython2-stdlib:armhf.
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Unpacking libpython2-stdlib:armhf (2.7.16-1) ...
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Unpacking libpython-stdlib:armhf (2.7.16-1) ...
Setting up libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ...
Setting up python2.7-minimal (2.7.16-2+deb10u1) ...
Setting up python2-minimal (2.7.16-1) ...
Selecting previously unselected package python2.
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Preparing to unpack .../python2_2.7.16-1_armhf.deb ...
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Setting up python-minimal (2.7.16-1) ...
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Selecting previously unselected package libpython3.7-minimal:armhf.
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Selecting previously unselected package python3.7-minimal.
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Setting up libssl1.1:armhf (1.1.1d-0+deb10u6) ...
Setting up libpython3.7-minimal:armhf (3.7.3-2+deb10u3) ...
Setting up libexpat1:armhf (2.2.6-2+deb10u1) ...
Setting up python3.7-minimal (3.7.3-2+deb10u3) ...
Selecting previously unselected package python3-minimal.
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Selecting previously unselected package libmpdec2:armhf.
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Selecting previously unselected package libpython3.7-stdlib:armhf.
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Unpacking libpython3.7-stdlib:armhf (3.7.3-2+deb10u3) ...
Selecting previously unselected package python3.7.
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Unpacking python3.7 (3.7.3-2+deb10u3) ...
Selecting previously unselected package libpython3-stdlib:armhf.
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Setting up python3-minimal (3.7.3-1) ...
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Unpacking python3 (3.7.3-1) ...
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Unpacking sensible-utils (0.0.12) ...
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Unpacking libmagic-mgc (1:5.35-4+deb10u2) ...
Selecting previously unselected package libmagic1:armhf.
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Unpacking libmagic1:armhf (1:5.35-4+deb10u2) ...
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Unpacking file (1:5.35-4+deb10u2) ...
Selecting previously unselected package gettext-base.
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Unpacking gettext-base (0.19.8.1-9) ...
Selecting previously unselected package libsigsegv2:armhf.
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Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../07-m4_1.4.18-2_armhf.deb ...
Unpacking m4 (1.4.18-2) ...
Selecting previously unselected package autoconf.
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Unpacking autoconf (2.69-11) ...
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Unpacking autotools-dev (20180224.1) ...
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Unpacking automake (1:1.16.1-4) ...
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Unpacking autopoint (0.19.8.1-9) ...
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Unpacking libkeyutils1:armhf (1.6-6) ...
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Unpacking libkrb5support0:armhf (1.17-3+deb10u1) ...
Selecting previously unselected package libk5crypto3:armhf.
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Unpacking libk5crypto3:armhf (1.17-3+deb10u1) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../15-libkrb5-3_1.17-3+deb10u1_armhf.deb ...
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No schema files found: doing nothing.
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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-1.16 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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Processing triggers for libc-bin (2.28-10) ...
Reading package lists...
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fakeroot is already the newest version (1.23-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: Running cd /build/python-pysam-0.15.2+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pysam_0.15.2+ds-2_source.changes
dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.15.2+ds-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <michael.crusoe@gmail.com>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/build/python-pysam-0.15.2+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
#find . -name "*.bam" -delete # which deletes files tested
rm -rf tests/pysam_test_work \
tests/example_htslib.gtf.gz.tbi \
tests/log.txt \
tests/test.bam \
tests/_compile_test.c \
tests/pysam_ex2.sam \
tests/__pycache__ \
pysam/calignmentfile.c \
pysam/cbcf.c \
tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
tests/pysam_data/ex1.fa.gz \
tests/pysam_data/ex1.fa.gz.gzi \
tests/pysam_data/ex1_csi.bam.csi
rm -rf .pytest_cache/
dh clean --with python2,python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/python-pysam-0.15.2+ds'
dh_auto_clean
I: pybuild base:217: python2.7 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
I: pybuild base:217: python3.7 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.7' does not exist -- can't clean it
rm -f \
pysam/config.py \
pysam/config.h \
pysam/lib*.c \
samtools/config.h \
bcftools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/build/python-pysam-0.15.2+ds'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules build
dh build --with python2,python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:217: python2.7 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:217: python3.7 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/utils.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/config.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/version.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/bcftools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/samtools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/Pileup.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/htslib_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libchtslib.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
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 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+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/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcsamtools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-2.7/samtools
creating build/temp.linux-armhf-2.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-armhf-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+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_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.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/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcbcftools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
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 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-armhf-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In function ‘init_data’,
inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:810:5:
bcftools/vcfcall.c.pysam.c:423:39: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:29,
from /usr/include/htslib/vcf.h:40,
from bcftools/vcfcall.c.pysam.c:34:
bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’:
/usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here
extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
^~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+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/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcutils.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’:
pysam/libcutils.c:6089:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration]
bcftools_set_stderr(__pyx_t_9);
^~~~~~~~~~~~~~~~~~~
samtools_set_stderr
pysam/libcutils.c:6233:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration]
bcftools_set_stdout_fn(__pyx_t_12);
^~~~~~~~~~~~~~~~~~~~~~
samtools_set_stdout_fn
pysam/libcutils.c:6244:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration]
bcftools_set_stdout(__pyx_t_9);
^~~~~~~~~~~~~~~~~~~
samtools_set_stdout
pysam/libcutils.c:6999:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration]
bcftools_set_optind(1);
^~~~~~~~~~~~~~~~~~~
samtools_set_optind
pysam/libcutils.c:7078:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration]
__pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
^~~~~~~~~~~~~
samtools_main
pysam/libcutils.c:7147:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration]
bcftools_unset_stderr();
^~~~~~~~~~~~~~~~~~~~~
samtools_unset_stderr
pysam/libcutils.c:7183:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration]
bcftools_unset_stdout();
^~~~~~~~~~~~~~~~~~~~~
samtools_unset_stdout
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:11401:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return PyInt_FromLong((long) value);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:5821:7: 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 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armhf-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcutils.o build/temp.linux-armhf-2.7/pysam/pysam_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcalignmentfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29332:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
__pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
~^~~~~~~~~~~~~~~~~~~
In file included from pysam/htslib_util.h:4,
from pysam/libcalignmentfile.c:619:
/usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27585:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
(void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:13687:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
(void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcsamfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcalignedsegment.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14226:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
(void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libctabix.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8631:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
__pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13697:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
__pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:13729:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
__pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:14099:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
__pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcfaidx.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcbcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:32813:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
__pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5,
from pysam/libcbcf.c:618:
/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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcbgzf.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libctabixproxies.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcvcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
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 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.74’:
pysam/libcvcf.c:24828:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
__pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
I: pybuild base:217: /usr/bin/python3 setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/utils.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/config.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/version.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/bcftools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/samtools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/Pileup.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/htslib_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
Fixing /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.7
creating build/temp.linux-armhf-3.7/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libchtslib.o build/temp.linux-armhf-3.7/pysam/htslib_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.7/samtools
creating build/temp.linux-armhf-3.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamtools.o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.7/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcftools.o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcutils.c -o build/temp.linux-armhf-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’:
pysam/libcutils.c:6089:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration]
bcftools_set_stderr(__pyx_t_9);
^~~~~~~~~~~~~~~~~~~
samtools_set_stderr
pysam/libcutils.c:6233:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration]
bcftools_set_stdout_fn(__pyx_t_12);
^~~~~~~~~~~~~~~~~~~~~~
samtools_set_stdout_fn
pysam/libcutils.c:6244:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration]
bcftools_set_stdout(__pyx_t_9);
^~~~~~~~~~~~~~~~~~~
samtools_set_stdout
pysam/libcutils.c:6999:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration]
bcftools_set_optind(1);
^~~~~~~~~~~~~~~~~~~
samtools_set_optind
pysam/libcutils.c:7078:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration]
__pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
^~~~~~~~~~~~~
samtools_main
pysam/libcutils.c:7147:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration]
bcftools_unset_stderr();
^~~~~~~~~~~~~~~~~~~~~
samtools_unset_stderr
pysam/libcutils.c:7183:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration]
bcftools_unset_stdout();
^~~~~~~~~~~~~~~~~~~~~
samtools_unset_stdout
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:526:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PyInt_FromLong PyLong_FromLong
^~~~~~~~~~~~~~~
pysam/libcutils.c:5821:7: note: ‘__pyx_v_retval’ was declared here
int __pyx_v_retval;
^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcutils.o build/temp.linux-armhf-3.7/pysam/pysam_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcsamtools.cpython-37m-arm-linux-gnueabihf -lcbcftools.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29332:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
__pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
~^~~~~~~~~~~~~~~~~~~
In file included from pysam/htslib_util.h:4,
from pysam/libcalignmentfile.c:619:
/usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27585:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
(void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:13687:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
(void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignmentfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14226:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
(void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libctabix.c -o build/temp.linux-armhf-3.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8631:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
__pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13697:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
__pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:13729:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
__pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
^~~~~~~~
pysam/libctabix.c:14099:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
__pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabix.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcfaidx.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:32813:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
__pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5,
from pysam/libcbcf.c:618:
/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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbgzf.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabixproxies.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.79’:
pysam/libcvcf.c:24828:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
__pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcvcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/python-pysam-0.15.2+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/build/python-pysam-0.15.2+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
[bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
[bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
[bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
[bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
[bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
[bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
[bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
[bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
[bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
[bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
[bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
[bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
[bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
[bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
[bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
[bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
[bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
[bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
[bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
[bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
[bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
[bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
[bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
[bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
[bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
[bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
[bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
[bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
[bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
[bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
[bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
[bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view -bS with_md.sam > with_md.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam
samtools view -bS tag_bug.sam > tag_bug.bam
samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam
samtools view -bS softclip.sam > softclip.bam
samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam
samtools view -bS test_unaligned.sam > test_unaligned.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS ex10.sam > ex10.bam
samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam
samtools view -bS example_empty_header.sam > example_empty_header.bam
samtools view -bS ex4.sam > ex4.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS issue100.sam > issue100.bam
samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam
samtools view -bS ex5.sam > ex5.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 ex6.sam > ex6.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 example_dash_in_chr.bam
samtools index tag_bug.bam
samtools index test_mapped_unmapped.bam
samtools index softclip.bam
samtools index example_empty_with_header.bam
samtools index test_unaligned.bam
samtools index ex9_fail.bam
samtools index ex10.bam
samtools index example_aligned_pairs.bam
samtools index example_empty_header.bam
samtools index ex4.bam
samtools index ex9_nofail.bam
samtools index issue100.bam
samtools index example_reverse_complement.bam
samtools index ex5.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 ex6.bam
samtools index example_user_header.bam
samtools index ex8.bam
samtools index ex3.bam
samtools view -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
rm with_md.sam
make[2]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data'
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz # create csi index
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -p vcf example_vcf40.vcf.gz # create tbi index
bcftools index example_vcf40.vcf.gz # create csi index
bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
tabix -p vcf gnomad_fixed.vcf.gz # create tbi index
bcftools index gnomad_fixed.vcf.gz # create csi index
bgzip < gnomad.vcf > gnomad.vcf.gz
tabix -p vcf gnomad.vcf.gz # create tbi index
bcftools index gnomad.vcf.gz # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf missing_genotypes.vcf.gz # create tbi index
bcftools index missing_genotypes.vcf.gz # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -p vcf example_vcf42.vcf.gz # create tbi index
bcftools index example_vcf42.vcf.gz # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index
bcftools index example_vcf42_only_header.vcf.gz # create csi index
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.bcf
bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools index gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
bcftools index gnomad.bcf
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf42_only_header.bcf
make[2]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:217: cd /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests
============================= test session starts ==============================
platform linux2 -- Python 2.7.16, pytest-3.10.1, py-1.7.0, pluggy-0.8.0 -- /usr/bin/python2.7
cachedir: .pytest_cache
rootdir: /build/python-pysam-0.15.2+ds, inifile: setup.cfg
collecting ... collected 926 items
tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection FAILED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection FAILED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED
tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_KN4mSB
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_nkYBPF
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_8PjA6N
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_OOTOH4
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_b7KnFX
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_AXLF88
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
[E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing SKIPPED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz
PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo PASSED
tests/VariantFile_test.py::TestParsing::testPos PASSED
tests/VariantFile_test.py::TestParsing::testQual PASSED
tests/VariantFile_test.py::TestParsing::testRef PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
tests/VariantFile_test.py::TestParsing::testStart PASSED
tests/VariantFile_test.py::TestParsing::testStop PASSED
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
FAILED
tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED
tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED
tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED
tests/compile_test.py::BAMTest::testCount PASSED
tests/compile_test.py::GTFTest::testCount PASSED
tests/faidx_test.py::TestFastaFile::testFetch PASSED
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
tests/faidx_test.py::TestFastaFile::testLength PASSED
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
tests/samtools_test.py::SamtoolsTest::testStatements PASSED
tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
tests/samtools_test.py::PysamTest::testStatements PASSED
tests/samtools_test.py::PysamTest::testUsage SKIPPED
tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::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_issue85::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
tests/tabix_test.py::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] GL should be declared as Number=G
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED
tests/tabix_test.py::TestCompression::testCompression PASSED
tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionSam::testCompression PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionBed::testCompression PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testCompression PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestGZFile::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED
tests/tabix_test.py::TestIterationWithComments::testAll PASSED
tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithComments::testReopening PASSED
tests/tabix_test.py::TestIterators::testClosedFile PASSED
tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED
tests/tabix_test.py::TestIterators::testIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED
tests/tabix_test.py::TestBed::testRead PASSED
tests/tabix_test.py::TestBed::testWrite PASSED
tests/tabix_test.py::TestVCFFromTabix::testRead PASSED
tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED
tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED
tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED
tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED
tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testScope PASSED
tests/tabix_test.py::TestContextManager::testManager PASSED
tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED
tests/tabixproxies_test.py::TestParser::testCopy PASSED
tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestParser::testRead PASSED
tests/tabixproxies_test.py::TestParser::testUnset PASSED
tests/tabixproxies_test.py::TestParser::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::testCopy PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGTF::testRead PASSED
tests/tabixproxies_test.py::TestGTF::testUnset PASSED
tests/tabixproxies_test.py::TestGTF::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::testCopy PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testRead PASSED
tests/tabixproxies_test.py::TestGFF3::testUnset PASSED
tests/tabixproxies_test.py::TestGFF3::testWrite PASSED
tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED
tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED
tests/test_samtools_python.py::test_bedcov_split_lines PASSED
tests/test_samtools_python.py::test_idxstats_parse PASSED
tests/test_samtools_python.py::test_bedcov PASSED
=================================== FAILURES ===================================
_________ TestSetTagGetTag.test_set_tag_with_automated_type_detection __________
self = <AlignedSegment_test.TestSetTagGetTag testMethod=test_set_tag_with_automated_type_detection>
def test_set_tag_with_automated_type_detection(self):
self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c")
self.check_tag('TT', -(1 << 7) - 1,
value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15) - 1,
value_type=None, alt_value_type="i")
> self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i")
tests/AlignedSegment_test.py:1213:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/AlignedSegment_test.py:1164: in check_tag
a.set_tag(tag, value, value_type=value_type)
pysam/libcalignedsegment.pyx:2232: in pysam.libcalignedsegment.AlignedSegment.set_tag
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: can't guess type or invalid type code specified: -2147483648 None
pysam/libcalignedsegment.pyx:2311: ValueError
_________ TestSetTagsGetTag.test_set_tag_with_automated_type_detection _________
self = <AlignedSegment_test.TestSetTagsGetTag testMethod=test_set_tag_with_automated_type_detection>
def test_set_tag_with_automated_type_detection(self):
self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c")
self.check_tag('TT', -(1 << 7) - 1,
value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15) - 1,
value_type=None, alt_value_type="i")
> self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i")
tests/AlignedSegment_test.py:1213:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/AlignedSegment_test.py:1242: in check_tag
a.set_tags([(tag, value, value_type)])
pysam/libcalignedsegment.pyx:2577: in pysam.libcalignedsegment.AlignedSegment.set_tags
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: could not deduce typecode for value -2147483648
pysam/libcalignedsegment.pyx:422: ValueError
_____________________ 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:592:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcbcf.pyx:3442: in pysam.libcbcf.VariantRecordSample.__setitem__
???
pysam/libcbcf.pyx:855: in pysam.libcbcf.bcf_format_set_value
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: invalid value for Integer format
pysam/libcbcf.pyx:588: TypeError
=============================== warnings summary ===============================
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/_compile_test.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator
/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated
ignore_truncation=True)
-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 3 failed, 906 passed, 17 skipped, 2 warnings in 701.74 seconds ========
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests
dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned exit code 13
make[1]: *** [debian/rules:32: override_dh_auto_test] Error 25
make[1]: Leaving directory '/build/python-pysam-0.15.2+ds'
make: *** [debian/rules:24: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/28455 and its subdirectories
Thu Sep 2 14:58:13 UTC 2021 W: No second build log, what happened?