Build log for python-pysam (0.20.0+ds-1) on armhf

python-pysam → 0.20.0+ds-1 → armhf → 2022-12-05 10:20:34

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd

+==============================================================================+
| python-pysam 0.20.0+ds-1 (armhf)             Mon, 05 Dec 2022 09:29:21 +0000 |
+==============================================================================+

Package: python-pysam
Version: 0.20.0+ds-1
Source Version: 0.20.0+ds-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-aeeb8a05-3f94-4106-86dc-3feda8db84e2' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.8 MB in 30s (934 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-pysam.git
Please use:
git clone https://salsa.debian.org/med-team/python-pysam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1423 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main python-pysam 0.20.0+ds-1 (dsc) [2531 B]
Get:2 http://172.17.4.1/private bookworm-staging/main python-pysam 0.20.0+ds-1 (tar) [1411 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main python-pysam 0.20.0+ds-1 (diff) [9864 B]
Fetched 1423 kB in 0s (3925 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-gF4fNq/python-pysam-0.20.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-gF4fNq' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-vEnLlH/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-vEnLlH/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-vEnLlH/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2679 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libpam-cap libperl5.34 netbase perl-modules-5.34 sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 80 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14774 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest
Filtered Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-vEnLlH/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-python-pysam-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Sources [580 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ Packages [648 B]
Fetched 2561 B in 1s (3522 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install python-pysam build dependencies (apt-based resolver)
------------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libpam-cap libperl5.34 netbase perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdextrautils bsdutils
  cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
  dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libblkid1 libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
  libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72
  libjs-jquery libjs-sphinxdoc libjs-underscore liblzma-dev liblzma5
  libmagic-mgc libmagic1 libmount1 libmpdec3 libncurses6 libnghttp2-14
  libpipeline1 libpsl5 libpython3-dev libpython3-stdlib libpython3.10
  libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib librtmp1
  libsmartcols1 libssh2-1 libsub-override-perl libtool libuchardet0 libuuid1
  libxml2 m4 man-db media-types mount po-debconf python3 python3-attr
  python3-dev python3-distutils python3-iniconfig python3-lib2to3
  python3-minimal python3-more-itertools python3-packaging
  python3-pkg-resources python3-pluggy python3-py python3-pyparsing
  python3-pytest python3-setuptools python3-tomli python3.10 python3.10-dev
  python3.10-minimal samtools tabix util-linux util-linux-extra xz-utils
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc python3-numpy python3-matplotlib
  texlive-latex-recommended cython-doc dh-make flit python3-build
  python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff
  libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
  librtmp-dev libssh2-1-dev pkg-config liblzma-doc cryptsetup-bin libtool-doc
  gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  nfs-common libmail-box-perl python3-doc python3-tk python3-venv
  python-attr-doc subversion python-pyparsing-doc python-setuptools-doc
  python3.10-venv python3.10-doc binfmt-support cwltool dosfstools kbd
  util-linux-locales
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
  libgpm2 publicsuffix libltdl-dev uuid-runtime libmail-sendmail-perl
  python3-pygments
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3
  debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
  libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72
  libjs-jquery libjs-sphinxdoc libjs-underscore liblzma-dev libmagic-mgc
  libmagic1 libmpdec3 libncurses6 libnghttp2-14 libpipeline1 libpsl5
  libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev
  libpython3.10-minimal libpython3.10-stdlib librtmp1 libssh2-1
  libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types
  po-debconf python3 python3-attr python3-dev python3-distutils
  python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools
  python3-packaging python3-pkg-resources python3-pluggy python3-py
  python3-pyparsing python3-pytest python3-setuptools python3-tomli python3.10
  python3.10-dev python3.10-minimal samtools
  sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
The following packages will be upgraded:
  bsdutils libblkid1 liblzma5 libmount1 libsmartcols1 libuuid1 mount
  util-linux util-linux-extra xz-utils
10 upgraded, 83 newly installed, 0 to remove and 70 not upgraded.
Need to get 38.8 MB of archives.
After this operation, 146 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vEnLlH/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdutils armhf 1:2.38.1-4 [83.9 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libsmartcols1 armhf 2.38.1-4 [91.6 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf util-linux-extra armhf 2.38.1-4 [98.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf util-linux armhf 2.38.1-4 [1062 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf mount armhf 2.38.1-4 [126 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.8-3 [769 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.8-3 [1478 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf liblzma5 armhf 5.2.8-0.0 [175 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libuuid1 armhf 2.38.1-4 [27.1 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.8-3 [1597 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.8-3 [506 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libblkid1 armhf 2.38.1-4 [131 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libmount1 armhf 2.38.1-4 [144 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf xz-utils armhf 5.2.8-0.0 [333 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.86.0-2 [318 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-3 [367 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf bcftools armhf 1.13-1 [565 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf cython3 armhf 0.29.32-2 [1218 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.1 [80.8 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.1 [941 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf dh-exec armhf 0.27+b1 [23.4 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.8-1 [139 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.86.0-2 [394 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.5.0-1 [130 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.8-0.0 [232 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.16+ds-3 [1479 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-2 [116 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.5.0-4 [142 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10 armhf 3.10.8-3 [1458 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-dev armhf 3.10.8-3 [2935 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.10.6-1 [22.0 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf python3-attr all 22.1.0-1 [64.1 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf python3.10-dev armhf 3.10.8-3 [509 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.10.6-1 [25.4 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf python3-pyparsing all 3.0.7-3 [136 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 21.3-1.1 [34.2 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 65.5.0-1 [278 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf python3-py all 1.11.0-1 [89.2 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf python3-tomli all 2.0.1-2 [17.9 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-4 [218 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 65.5.0-1 [519 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.16.1-1 [559 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf tabix armhf 1.16+ds-3 [365 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up python3-pytest (7.1.2-4) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 bcftools_1.13-1 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 cython3_0.29.32-2 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.11.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-exec_0.27+b1 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-10 gettext-base_0.21-10 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblkid1_2.38.1-4 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcurl3-gnutls_7.86.0-2 libcurl4-gnutls-dev_7.86.0-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.11.1 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-2 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-3 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libicu72_72.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_4.5.0-4 libjs-underscore_1.13.4~dfsg+~1.11.4-2 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.13+dfsg-2+rpi1 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.2.8-0.0 liblzma5_5.2.8-0.0 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.7-1 libpsl5_0.21.0-1.2 libpython3-dev_3.10.6-1 libpython3-stdlib_3.10.6-1 libpython3.10_3.10.8-3 libpython3.10-dev_3.10.8-3 libpython3.10-minimal_3.10.8-3 libpython3.10-stdlib_3.10.8-3 libreadline8_8.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-4 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.5-4 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-4 libxml2_2.9.14+dfsg-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-4 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-attr_22.1.0-1 python3-dev_3.10.6-1 python3-distutils_3.10.8-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-1 python3-more-itertools_8.10.0-2 python3-packaging_21.3-1.1 python3-pkg-resources_65.5.0-1 python3-pluggy_1.0.0+repack-1 python3-py_1.11.0-1 python3-pyparsing_3.0.7-3 python3-pytest_7.1.2-4 python3-setuptools_65.5.0-1 python3-tomli_2.0.1-2 python3.10_3.10.8-3 python3.10-dev_3.10.8-3 python3.10-minimal_3.10.8-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 samtools_1.16.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tabix_1.16+ds-3 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 xz-utils_5.2.8-0.0 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.2TN5K1nv/trustedkeys.kbx': General error
gpgv: Signature made Tue Nov 29 21:22:53 2022 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./python-pysam_0.20.0+ds-1.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.20.0+ds
dpkg-source: info: unpacking python-pysam_0.20.0+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.20.0+ds-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip_test_remote.patch
dpkg-source: info: applying clean_less
dpkg-source: info: applying skip-test-on-32-bit.patch

Check disc space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-aeeb8a05-3f94-4106-86dc-3feda8db84e2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.20.0+ds-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/pysam_data'
rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \
all.stamp *~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/cbcf_data'
rm -f all.stamp *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*.bam" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "pysam_uncompressed.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c \
	tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
	tests/pysam_data/ex1.fa.gz \
	tests/pysam_data/ex1.fa.gz.gzi \
	tests/pysam_data/ex1_csi.bam.csi
rm -rf .pytest_cache/
dh clean --with python3 --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds'
dh_auto_clean
I: pybuild base:240: python3.10 setup.py clean 
/<<BUILDDIR>>/python-pysam-0.20.0+ds/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  from distutils import log
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
  warnings.warn(
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.10' does not exist -- can't clean it
rm -f \
	pysam/config.py \
	pysam/config.h \
	pysam/lib*.c \
	samtools/config.h \
	bcftools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:240: python3.10 setup.py config 
/<<BUILDDIR>>/python-pysam-0.20.0+ds/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  from distutils import log
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
  warnings.warn(
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build 
/<<BUILDDIR>>/python-pysam-0.20.0+ds/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  from distutils import log
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
  warnings.warn(
/usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/version.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/py.typed -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcalignedsegment.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcalignmentfile.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcbcf.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcbcftools.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcbgzf.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcfaidx.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libchtslib.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcsamfile.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcsamtools.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libctabix.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libctabixproxies.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcutils.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/libcvcf.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
copying pysam/version.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/consensus_pileup.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/splaysort.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/abuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/dbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/dist.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/extsort.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/str_finder.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/utlist.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libchtslib.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcsamtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcbcftools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcutils.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcalignmentfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2573:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2578:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2583:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2622:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2627:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2632:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcsamfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcalignedsegment.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libctabix.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcfaidx.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcbcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcbgzf.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libctabixproxies.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam/libcvcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armhf-cpython-310
creating build/temp.linux-armhf-cpython-310/pysam
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/htslib_util.c -o build/temp.linux-armhf-cpython-310/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libchtslib.c -o build/temp.linux-armhf-cpython-310/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/htslib_util.o build/temp.linux-armhf-cpython-310/pysam/libchtslib.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-cpython-310/samtools
creating build/temp.linux-armhf-cpython-310/samtools/lz4
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcsamtools.c -o build/temp.linux-armhf-cpython-310/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/coverage.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-cpython-310/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/reference.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-cpython-310/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcsamtools.o build/temp.linux-armhf-cpython-310/samtools/amplicon_stats.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_color.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_consensus.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_fastq.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_import.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_index.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_md.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_samples.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_split.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bamtk.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bedcov.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/bedidx.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/consensus_pileup.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/coverage.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/cut_target.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/dict.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/faidx.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/lz4/lz4.o build/temp.linux-armhf-cpython-310/samtools/padding.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/phase.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/reference.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/sam_view.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/sample.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/samtools.pysam.o build/temp.linux-armhf-cpython-310/samtools/stats.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-cpython-310/samtools/tmp_file.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-cpython-310/bcftools
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/abuf.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/cols.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/dist.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/extsort.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
  751 |         ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));  // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
                 from /usr/include/htslib/hts.h:37,
                 from /usr/include/htslib/vcf.h:39,
                 from bcftools/vcfmerge.c.pysam.c:35:
/usr/include/stdlib.h:543:14: note: in a call to allocation function ‘calloc’ declared here
  543 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-cpython-310/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcbcftools.c -o build/temp.linux-armhf-cpython-310/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/bcftools/HMM.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/abuf.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/bcftools.pysam.o build/temp.linux-armhf-cpython-310/bcftools/bin.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/ccall.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/cols.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/consensus.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/convert.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/csq.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/dist.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/em.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/extsort.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/filter.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/hclust.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/kmin.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/main.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/mcall.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/prob1.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/regidx.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/reheader.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/str_finder.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/tabix.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfhead.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-cpython-310/bcftools/version.c.pysam.o build/temp.linux-armhf-cpython-310/pysam/libcbcftools.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcutils.c -o build/temp.linux-armhf-cpython-310/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/pysam_util.c -o build/temp.linux-armhf-cpython-310/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcutils.o build/temp.linux-armhf-cpython-310/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcsamtools.cpython-310-arm-linux-gnueabihf -lcbcftools.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-cpython-310/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcsamfile.c -o build/temp.linux-armhf-cpython-310/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-cpython-310/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libctabix.c -o build/temp.linux-armhf-cpython-310/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcfaidx.c -o build/temp.linux-armhf-cpython-310/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcbcf.c -o build/temp.linux-armhf-cpython-310/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcbgzf.c -o build/temp.linux-armhf-cpython-310/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbgzf.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-cpython-310/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.10 -c pysam/libcvcf.c -o build/temp.linux-armhf-cpython-310/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.constprop’:
pysam/libcvcf.c:25229:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized]
25229 |   __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcvcf.c:19949:10: note: ‘__pyx_v_qual’ was declared here
19949 |   double __pyx_v_qual;
      |          ^~~~~~~~~~~~
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-310-arm-linux-gnueabihf -lcutils.cpython-310-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.cpython-310-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz
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 --no-PG -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view --no-PG -bo ex2.bam ex2.sam
samtools index ex2.bam
samtools calmd --no-PG --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 --no-PG -bo with_md.bam with_md.sam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view --no-PG -bu -o uncompressed.bam ex2.sam
samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam
samtools view --no-PG -bo MM-double.bam MM-double.sam
samtools view --no-PG -bo MM-multi.bam MM-multi.sam
samtools view --no-PG -bo MM-orient.bam MM-orient.sam
samtools view --no-PG -bo ex10.bam ex10.sam
samtools view --no-PG -bo ex3.bam ex3.sam
samtools view --no-PG -bo ex4.bam ex4.sam
samtools view --no-PG -bo ex5.bam ex5.sam
samtools view --no-PG -bo ex6.bam ex6.sam
samtools view --no-PG -bo ex8.bam ex8.sam
samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam
samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam
samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam
samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam
samtools view --no-PG -bo example_btag.bam example_btag.sam
samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam
samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam
samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam
samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam
touch tmp.list
samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam
rm -f tmp.list
samtools view --no-PG -bo issue100.bam issue100.sam
samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam
samtools view --no-PG -bo softclip.bam softclip.sam
samtools view --no-PG -bo tag_bug.bam tag_bug.sam
samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam
samtools view --no-PG -bo test_query_position.bam test_query_position.sam
samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam
samtools index MM-chebi.bam
samtools index MM-double.bam
samtools index MM-multi.bam
samtools index MM-orient.bam
samtools index ex10.bam
samtools index ex3.bam
samtools index ex4.bam
samtools index ex5.bam
samtools index ex6.bam
samtools index ex8.bam
samtools index ex9_fail.bam
samtools index ex9_nofail.bam
samtools index ex_spliced.bam
samtools index example_aligned_pairs.bam
samtools index example_btag.bam
samtools index example_dash_in_chr.bam
samtools index example_empty_header.bam
samtools index example_empty_with_header.bam
samtools index example_reverse_complement.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index issue100.bam
samtools index rg_with_tab.bam
samtools index softclip.bam
samtools index tag_bug.bam
samtools index test_mapped_unmapped.bam
samtools index test_query_position.bam
samtools index test_unaligned.bam
samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam
samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam
samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam
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
dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1
1+0 records in
1+0 records out
122292 bytes (122 kB, 119 KiB) copied, 0.00132972 s, 92.0 MB/s
(bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam
grep "^@" ex2.sam | samtools view --no-PG -bo 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
touch all.stamp
rm with_md.sam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/cbcf_data'
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 < 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
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_vcf43.vcf > example_vcf43.vcf.gz
tabix -p vcf example_vcf43.vcf.gz    # create tbi index
bcftools index example_vcf43.vcf.gz  # create csi index
bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz
tabix -p vcf example_vcf43_with_utf8.vcf.gz    # create tbi index
bcftools index example_vcf43_with_utf8.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 < 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 < 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
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.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
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_vcf43.vcf.gz -o example_vcf43.bcf
bcftools index example_vcf43.bcf
bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf
bcftools index example_vcf43_with_utf8.bcf
bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
bcftools index gnomad.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 missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
touch all.stamp
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:240: cd /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build; python3.10 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3.10
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/python-pysam-0.20.0+ds, configfile: setup.cfg
collecting ... collected 949 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::testUpdateQual 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_padding_with_seq 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::TestBaseModifications::testChebi PASSED
tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED
tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED
tests/AlignedSegment_test.py::TestBaseModifications::testOrient 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 [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp___enter___baanal86negative_integers.bam'
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 PASSED
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 PASSED
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 [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mhuou0km'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mhuou0km
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_jiql8m72'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_jiql8m72
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_wt_xd9nv
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ig15c9ce'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ig15c9ce
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_4deap5rh'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_4deap5rh
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_fmgc_xpp
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 PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [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::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 [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_3i2l5djntmp_ex2.bam'
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" : No such file or directory
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 [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_lalpj_vktmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_2etvx7eztmp_multi.bam'
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" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
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::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/0example_no_seq_in_header.bam'
PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam'
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::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/ex2_truncated.bam'
[E::bgzf_read_block] Failed to read BGZF block data at offset 105180 expected 17578 bytes; hread returned 17094
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/pysam_data/ex2_corrupt.bam'
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" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_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::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_fcv89d3dtmp_largecigar.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 PASSED
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::testEmptyFileVCFFromPath PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory
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::testAllelesVariantTypes PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo Fatal Python error: Bus error

Current thread 0xb6f0d020 (most recent call first):
  File "/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/VariantFile_test.py", line 400 in <listcomp>
  File "/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/VariantFile_test.py", line 400 in testInfo
  File "/usr/lib/python3.10/unittest/case.py", line 549 in _callTestMethod
  File "/usr/lib/python3.10/unittest/case.py", line 591 in run
  File "/usr/lib/python3.10/unittest/case.py", line 650 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 327 in runtest
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 166 in pytest_runtest_call
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 259 in <lambda>
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 338 in from_call
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 258 in call_runtest_hook
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 219 in call_and_report
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 130 in runtestprotocol
  File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 111 in pytest_runtest_protocol
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in pytest_runtestloop
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 322 in _main
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 268 in wrap_session
  File "/usr/lib/python3/dist-packages/_pytest/main.py", line 315 in pytest_cmdline_main
  File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 164 in main
  File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 187 in console_main
  File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 5 in <module>
  File "/usr/lib/python3.10/runpy.py", line 86 in _run_code
  File "/usr/lib/python3.10/runpy.py", line 196 in _run_module_as_main

Extension modules: pysam.libcutils, pysam.libchtslib, pysam.libcsamtools, pysam.libcbcftools, pysam.libcfaidx, pysam.libctabixproxies, pysam.libctabix, pysam.libcalignmentfile, pysam.libcalignedsegment, pysam.libcsamfile, pysam.libcvcf, pysam.libcbcf, pysam.libcbgzf, Cython.Plex.Actions, Cython.Plex.Scanners, Cython.Compiler.Scanning, Cython.Tempita._tempita, Cython.Compiler.Visitor, Cython.Compiler.FlowControl, _compile_test (total: 20)
Bus error
E: pybuild pybuild:379: test: plugin distutils failed with: exit code=135: cd /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build; python3.10 -m pytest tests
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 returned exit code 13
make[1]: *** [debian/rules:30: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.20.0+ds'
make: *** [debian/rules:22: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2022-12-05T10:20:30Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 0
Build-Time: 2350
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 659
Job: python-pysam_0.20.0+ds-1
Machine Architecture: armhf
Package: python-pysam
Package-Time: 3069
Source-Version: 0.20.0+ds-1
Space: 0
Status: failed
Version: 0.20.0+ds-1
--------------------------------------------------------------------------------
Finished at 2022-12-05T10:20:30Z
Build needed 00:00:00, 0k disc space
Raspbian Package Auto-Building

Build log for python-pysam (0.20.0+ds-1) on armhf
