upstream has closed issue #91[1] and it should work with Debian
packaged htslib. Thus I've added libhts-dev to Build-Depends
but the build finally fails with
...
I: pybuild base:217: cd /build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose -v.
Failure: ImportError (/build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: undefined symbol: bcf_float_missing) ... ERROR
======================================================================
ERROR: Failure: ImportError (/build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: undefined symbol: bcf_float_missing)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__init__.py", line 1, in <module>
from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: /build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: undefined symbol: bcf_float_missing
----------------------------------------------------------------------
Ran 1 test in 0.006s
FAILED (errors=1)
E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd /build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose -v.
...
Could someone please have a look?
I have started to investigate this: the fail is related to recent upstream
changes [1] and [2]. I have no time to look deeper into this right now,
maybe at the end of the week, if nobody resolve it earlier.
PS: I've just closed #904836. I'd like to repeat my plea that people
join our Advent calendar bug squashing. This was the easiest bug so
far since it was closed with a previous upload but forgotten in
d/changelog.
oh, I had not noticed this bug then.
It would really help if others could check for those
easy ones in our list of bugs. Thank you.
Sorry, but I am participating in another squashing, trying to finish all
the assignments I had to do for my university :-P
Kind regards,
Liubov