Raspbian Package Auto-Building

python-pysam → 0.20.0+ds-3 → armhf → 2023-01-07 19:53:27

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

+==============================================================================+
| python-pysam 0.20.0+ds-3 (armhf)             Sat, 07 Jan 2023 18:24:07 +0000 |
+==============================================================================+

Package: python-pysam
Version: 0.20.0+ds-3
Source Version: 0.20.0+ds-3
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-bc6c784f-6401-4255-8c76-f6b2ff6fe5b3' 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 27.9 MB in 30s (944 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-3 (dsc) [1806 B]
Get:2 http://172.17.4.1/private bookworm-staging/main python-pysam 0.20.0+ds-3 (tar) [1411 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main python-pysam 0.20.0+ds-3 (diff) [10.6 kB]
Fetched 1423 kB in 0s (3567 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-PwA0Sx/python-pysam-0.20.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-PwA0Sx' 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-KDxGS3/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-KDxGS3/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-KDxGS3/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-KDxGS3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2940 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 netbase 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 35 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12958 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-all-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-all-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-KDxGS3/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-KDxGS3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Sources [582 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ Packages [648 B]
Fetched 2563 B in 1s (3579 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 netbase
Use 'apt autoremove' to remove them.
The following additional 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 libncursesw6 libnghttp2-14 libpipeline1
  libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10
  libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.11
  libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib librtmp1
  libssh2-1 libsub-override-perl libtinfo6 libtool libuchardet0 libxml2 m4
  man-db media-types ncurses-base ncurses-bin po-debconf python3 python3-all
  python3-all-dev 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-pytest
  python3-setuptools python3-tomli python3.10 python3.10-dev
  python3.10-minimal python3.11 python3.11-dev python3.11-minimal samtools
  tabix 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 libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc
  subversion python-setuptools-doc python3.10-venv python3.10-doc
  binfmt-support python3.11-venv python3.11-doc cwltool
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
  libgpm2 publicsuffix libltdl-dev 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-all-dev libpython3-dev libpython3-stdlib libpython3.10
  libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.11
  libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib librtmp1
  libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
  media-types po-debconf python3 python3-all python3-all-dev 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-pytest
  python3-setuptools python3-tomli python3.10 python3.10-dev
  python3.10-minimal python3.11 python3.11-dev python3.11-minimal samtools
  sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
The following packages will be upgraded:
  libncursesw6 libtinfo6 ncurses-base ncurses-bin
4 upgraded, 92 newly installed, 0 to remove and 31 not upgraded.
Need to get 48.5 MB of archives.
After this operation, 192 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KDxGS3/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf ncurses-bin armhf 6.4-1 [414 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf ncurses-base all 6.4-1 [261 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.9-1 [769 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.9-1 [1477 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-3 [25.5 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libtinfo6 armhf 6.4-1 [316 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libncursesw6 armhf 6.4-1 [106 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.9-1 [1597 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.9-1 [509 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-3 [8588 B]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-3 [25.2 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-minimal armhf 3.11.1-2 [796 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf python3.11-minimal armhf 3.11.1-2 [1678 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.51.0-1 [60.5 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.87.0-1 [327 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-3 [367 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf bcftools armhf 1.13-1 [565 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf cython3 armhf 0.29.32-2 [1218 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.4 [942 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf dh-exec armhf 0.27+b1 [23.4 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.8-1 [139 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.87.0-1 [405 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.5.0-1 [130 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.4.0-0.1 [240 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.16+ds-3 [1479 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 5.3.0-2 [130 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.4-1 [79.8 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10 armhf 3.10.9-1 [1462 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-dev armhf 3.10.9-1 [2926 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.10.6-3 [8820 B]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-stdlib armhf 3.11.1-2 [1622 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11 armhf 3.11.1-2 [1666 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libpython3.11-dev armhf 3.11.1-2 [3375 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libpython3-all-dev armhf 3.10.6-3 [1072 B]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf python3.11 armhf 3.11.1-2 [567 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf python3-all armhf 3.10.6-3 [1064 B]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf python3.10-dev armhf 3.10.9-1 [512 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.10.6-3 [26.0 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf python3.11-dev armhf 3.11.1-2 [618 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf python3-all-dev armhf 3.10.6-3 [1076 B]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf python3-attr all 22.2.0-1 [65.4 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 22.0-2 [32.2 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 65.5.0-1.1 [278 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf python3-py all 1.11.0-1 [89.2 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf python3-tomli all 2.0.1-2 [17.9 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-4 [218 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 65.5.0-1.1 [519 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.16.1-1 [559 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf tabix armhf 1.16+ds-3 [365 kB]
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Setting up cython3 (0.29.32-2) ...
Setting up libpython3.10-dev:armhf (3.10.9-1) ...
Setting up python3-pluggy (1.0.0+repack-1) ...
Setting up python3.10-dev (3.10.9-1) ...
Setting up python3-lib2to3 (3.10.8-1) ...
Setting up python3-pkg-resources (65.5.0-1.1) ...
Setting up python3-distutils (3.10.8-1) ...
Setting up dh-python (5.20220819+rpi1) ...
Setting up python3-more-itertools (8.10.0-2) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-attr (22.2.0-1) ...
Setting up libpython3-dev:armhf (3.10.6-3) ...
Setting up python3-setuptools (65.5.0-1.1) ...
Setting up python3-tomli (2.0.1-2) ...
Setting up python3-py (1.11.0-1) ...
Setting up python3.11-dev (3.11.1-2) ...
Setting up python3-pytest (7.1.2-4) ...
Setting up python3-all (3.10.6-3) ...
Setting up debhelper (13.11.4) ...
Setting up dh-exec (0.27+b1) ...
Setting up libpython3-all-dev:armhf (3.10.6-3) ...
Setting up python3-dev (3.10.6-3) ...
Setting up python3-all-dev (3.10.6-3) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.36-6+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_2.39.50.20221208-5+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-10+rpi1 gcc-12_12.2.0-10+rpi1 libc6-dev_2.36-6+rpi1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 linux-libc-dev_6.0.12-1+rpi1
Package versions: adduser_3.129 apt_2.5.4 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_5.2-2 bcftools_1.13-1 binutils_2.39.50.20221208-5+rpi1 binutils-arm-linux-gnueabihf_2.39.50.20221208-5+rpi1 binutils-common_2.39.50.20221208-5+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_12.2.0-10+rpi1 cython3_0.29.32-2 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.4 debianutils_5.7-0.4 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_2.2.40-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.15-1 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_12.2.0-10+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-10+rpi1 gcc-12-base_12.2.0-10+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_2.2.40-1 gnupg-l10n_2.2.40-1 gnupg-utils_2.2.40-1 gpg_2.2.40-1 gpg-agent_2.2.40-1 gpg-wks-client_2.2.40-1 gpg-wks-server_2.2.40-1 gpgconf_2.2.40-1 gpgsm_2.2.40-1 gpgv_2.2.40-1 grep_3.8-3 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_3:20221126-1 krb5-locales_1.20.1-1 libacl1_2.3.1-2 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libasan8_12.2.0-10+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-10+rpi1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39.50.20221208-5+rpi1 libblkid1_2.38.1-4 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-6+rpi1 libc-dev-bin_2.36-6+rpi1 libc6_2.36-6+rpi1 libc6-dev_2.36-6+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-10+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libctf-nobfd0_2.39.50.20221208-5+rpi1 libctf0_2.39.50.20221208-5+rpi1 libcurl3-gnutls_7.87.0-1 libcurl4-gnutls-dev_7.87.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.265 libdebhelper-perl_13.11.4 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_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-2 libgcc-12-dev_12.2.0-10+rpi1 libgcc-s1_12.2.0-10+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-10+rpi1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-1 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 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_5.3.0-2 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 libksba8_1.6.2-4 libldap-2.5-0_2.5.13+dfsg-2+rpi1+b1 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.4.0-0.1 liblzma5_5.4.0-0.1 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_6.4-1 libncursesw6_6.4-1 libnettle8_3.8.1-2 libnghttp2-14_1.51.0-1 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_10.40-3 libpcre3_2:8.39-14 libperl5.36_5.36.0-6 libpipeline1_1.5.7-1 libpsl5_0.21.0-1.2 libpython3-all-dev_3.10.6-3 libpython3-dev_3.10.6-3 libpython3-stdlib_3.10.6-3 libpython3.10_3.10.9-1 libpython3.10-dev_3.10.9-1 libpython3.10-minimal_3.10.9-1 libpython3.10-stdlib_3.10.9-1 libpython3.11_3.11.1-2 libpython3.11-dev_3.11.1-2 libpython3.11-minimal_3.11.1-2 libpython3.11-stdlib_3.11.1-2 libreadline8_8.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 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_3.40.0-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.2-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.4-1 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_12.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_252.2-1+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_6.0.12-1+rpi1 login_1:4.13+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_7.1-1 ncurses-base_6.4-1 ncurses-bin_6.4-1 netbase_6.4 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-6 perl-base_5.36.0-6 perl-modules-5.36_5.36.0-6 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python3_3.10.6-3 python3-all_3.10.6-3 python3-all-dev_3.10.6-3 python3-attr_22.2.0-1 python3-dev_3.10.6-3 python3-distutils_3.10.8-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-3 python3-more-itertools_8.10.0-2 python3-packaging_22.0-2 python3-pkg-resources_65.5.0-1.1 python3-pluggy_1.0.0+repack-1 python3-py_1.11.0-1 python3-pytest_7.1.2-4 python3-setuptools_65.5.0-1.1 python3-tomli_2.0.1-2 python3.10_3.10.9-1 python3.10-dev_3.10.9-1 python3.10-minimal_3.10.9-1 python3.11_3.11.1-2 python3.11-dev_3.11.1-2 python3.11-minimal_3.11.1-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.2 rpcsvc-proto_1.4.3-1 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_3.05-7 tabix_1.16+ds-3 tar_1.34+dfsg-1 tzdata_2022f-1 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.H5rq0aeD/trustedkeys.kbx': General error
gpgv: Signature made Sat Dec 31 17:45:09 2022 UTC
gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./python-pysam_0.20.0+ds-3.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-3.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
dpkg-source: info: applying disable-tests-python3.11.patch
dpkg-source: info: applying python3.11.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-bc6c784f-6401-4255-8c76-f6b2ff6fe5b3
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-3
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: python3.11 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
I: pybuild base:240: python3.10 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.20.0+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: python3.11 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:240: python3.10 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3.11 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/version.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/py.typed -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignedsegment.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcalignmentfile.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcf.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbcftools.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcbgzf.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcfaidx.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libchtslib.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamfile.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcsamtools.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabix.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libctabixproxies.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcutils.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/libcvcf.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
copying pysam/version.pyi -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/consensus_pileup.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/splaysort.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/abuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/dbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/dist.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/extsort.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/str_finder.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/utlist.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_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-311
creating build/temp.linux-armhf-cpython-311/pysam
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/htslib_util.c -o build/temp.linux-armhf-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libchtslib.c -o build/temp.linux-armhf-cpython-311/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-311/pysam/htslib_util.o build/temp.linux-armhf-cpython-311/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_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-cpython-311/samtools
creating build/temp.linux-armhf-cpython-311/samtools/lz4
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcsamtools.c -o build/temp.linux-armhf-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/reference.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-cpython-311/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-311/pysam/libcsamtools.o build/temp.linux-armhf-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/dict.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/lz4/lz4.o build/temp.linux-armhf-cpython-311/samtools/padding.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/phase.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/reference.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/sample.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/samtools.pysam.o build/temp.linux-armhf-cpython-311/samtools/stats.c.pysam.o build/temp.linux-armhf-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-cpython-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-cpython-311/bcftools
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-cpython-311/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:556:14: note: in a call to allocation function ‘calloc’ declared here
  556 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcbcftools.c -o build/temp.linux-armhf-cpython-311/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-311/bcftools/HMM.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-armhf-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/em.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/main.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-cpython-311/bcftools/version.c.pysam.o build/temp.linux-armhf-cpython-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcutils.c -o build/temp.linux-armhf-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/pysam_util.c -o build/temp.linux-armhf-cpython-311/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-311/pysam/libcutils.o build/temp.linux-armhf-cpython-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcsamtools.cpython-311-arm-linux-gnueabihf -lcbcftools.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:28511:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
28511 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:14228:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14228 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.20.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-armhf-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14652:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14652 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libctabix.c -o build/temp.linux-armhf-cpython-311/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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcfaidx.c -o build/temp.linux-armhf-cpython-311/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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcbcf.c -o build/temp.linux-armhf-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’:
pysam/libcbcf.c:68189:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
68189 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’:
pysam/libcbcf.c:67914:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
67914 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’:
pysam/libcbcf.c:73032:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
73032 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’:
pysam/libcbcf.c:35496:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35496 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35522:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35522 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcbgzf.c -o build/temp.linux-armhf-cpython-311/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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-cpython-311/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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -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/python3.11 -c pysam/libcvcf.c -o build/temp.linux-armhf-cpython-311/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-311/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_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
I: pybuild base:240: /usr/bin/python3 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.20.0+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/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/__init__.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
copying samtools/samtools_config_vars.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
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
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
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
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:556:14: note: in a call to allocation function ‘calloc’ declared here
  556 | 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, 0.00148572 s, 82.3 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_3.11_pysam/build; python3.11 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.11.1, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3.11
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_3.11_pysam/build/tests/tmp/pysamtests_tmp___enter___5b5skfe6negative_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_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_2d83ccyn'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_2d83ccyn
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_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write__tz4jg74'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write__tz4jg74
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_w12aqscl
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_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_e3kcjc1l'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_e3kcjc1l
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_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_chusilld'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_chusilld
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_2buit841
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 SKIPPED
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_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_3dypt8_etmp_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_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_rehygu9ntmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_4b79h9_otmp_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_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_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_jo5k3m5ztmp_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 0xb6f66020 (most recent call first):
  File "/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/VariantFile_test.py", line 400 in <listcomp>
  File "/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/VariantFile_test.py", line 400 in testInfo
  File "/usr/lib/python3.11/unittest/case.py", line 579 in _callTestMethod
  File "/usr/lib/python3.11/unittest/case.py", line 623 in run
  File "/usr/lib/python3.11/unittest/case.py", line 678 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 "<frozen runpy>", line 88 in _run_code
  File "<frozen runpy>", line 198 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, _compile_test (total: 14)
Bus error
E: pybuild pybuild:379: test: plugin distutils failed with: exit code=135: cd /<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build; python3.11 -m pytest tests
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 3.10.9, 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___lna43wsonegative_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_tqsz7xfd'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_tqsz7xfd
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_hixjyram'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_hixjyram
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_mfmumi52
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_kt87ujws'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_kt87ujws
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_mspiroej'
/<<BUILDDIR>>/python-pysam-0.20.0+ds/.pybuild/cpython3_3.10_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mspiroej
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_w2z267lq
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_upi_s_00tmp_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_rup90imetmp_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_z7f80grltmp_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_o3pkl9pgtmp_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 0xb6f23020 (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 "3.11 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 2023-01-07T19:53:22Z

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: 4579
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 721
Job: python-pysam_0.20.0+ds-3
Machine Architecture: armhf
Package: python-pysam
Package-Time: 5355
Source-Version: 0.20.0+ds-3
Space: 0
Status: failed
Version: 0.20.0+ds-3
--------------------------------------------------------------------------------
Finished at 2023-01-07T19:53:22Z
Build needed 00:00:00, 0k disc space

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