Hi Andreas, On Sat, 15 Dec 2018 at 08:51, Andreas Tille <[email protected]> wrote:
> > 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 [1] https://github.com/brentp/cyvcf2/pull/93 [2] https://github.com/brentp/cyvcf2/commit/14d7443cba5234fd95b59760f834e8eb283bd8d2
