[Debian-med-packaging] Bug#879867: python3-pysam: import pysam throws ImportError undefined symbol: hts_log

[Diane Trout]

Package: python3-pysam
Version: 0.12.0.1+ds-3
Severity: normal

Dear Maintainer,

Importing pysam on testing in either python2 or python3 fails with this
error.

python3 -c 'import pysam'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 5, in <module>
    from pysam.libchtslib import *
  File "pysam/libchtslib.pyx", line 1, in init pysam.libchtslib
ImportError: /usr/lib/python3/dist-packages/pysam/libcbcftools.cpython-35m-x86_64-linux-gnu.so: undefined symbol: hts_log

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=871314
htslib: new version break python-pysam

When I upgrade to libhts2 to 1.5-1 the import error goes away.

I suspect the 0.12 version of pysam needs libhts2 (>= 1.5) and bug
871314 needs to be closed so libhts2 will migrate to testing.

Diane

-- System Information:
Debian Release: buster/sid
  APT prefers testing-debug
  APT policy: (500, 'testing-debug'), (500, 'stable-debug'), (500, 'testing'), (500, 'stable'), (110, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.13.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages python3-pysam depends on:
ii  libc6    2.24-17
ii  libhts2  1.4.1-5
ii  python3  3.5.3-3
ii  zlib1g   1:1.2.8.dfsg-5

python3-pysam recommends no packages.

python3-pysam suggests no packages.

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