Re: HTSlib code copy in python-pysam.
Hi Olivier,
On Mon, Aug 25, 2014 at 04:15:29PM +0200, Olivier Sallou wrote:
>
> On 08/25/2014 04:11 PM, Andreas Tille wrote:
> > Hi,
> >
> > any idea about the problem
> >
> > ImportError: /usr/lib/python2.7/dist-packages/pysam/csamfile.x86_64-linux-gnu.so: undefined symbol: sam_itr_queryi
> >
> > which is uncovered by the test? Should I seek help on debian-mentors
> > since I have no idea how to solve this. The problem also occures if I
> > disable the test at build time and try to run the test suite afterwards.
> there is definitly a missing library, did you try a ldd
>
> /usr/lib/python2.7/dist-packages/pysam/csamfile.x86_64-linux-gnu.so
>
>
> it should show the expected links (found or not).
I checked this and all libraries are available.
> If everything is found, then it is a matter of library version not
> exporting the same symbols....
Hmmm, well, it might be that this is the case. The internal code copy
has:
$ cat htslib/version.h
#define HTS_VERSION "0.0.1"
While libhts0 in Debian is 0.2.0~rc3. Any idea (except just to stick to
the internal code copy?
Kind regards
Andreas.
> > Kind regards
> >
> > Andreas.
> >
> > On Wed, Aug 20, 2014 at 12:24:48PM +0200, Andreas Tille wrote:
> >> Hi Charles,
> >>
> >> On Wed, Aug 20, 2014 at 07:08:40PM +0900, Charles Plessy wrote:
> >>> Le Wed, Aug 20, 2014 at 07:06:53PM +0900, Charles Plessy a écrit :
> >>>> Le Wed, Aug 20, 2014 at 11:10:32AM +0200, Andreas Tille a écrit :
> >>>>> --- a/setup.py
> >>>>> +++ b/setup.py
> >>>>> @@ -32,7 +32,7 @@ IS_PYTHON3 = sys.version_info[0] >= 3
> >>>>> # pysam.
> >>>>> # external: use shared libhts.so compiled outside of
> >>>>> # pysam
> >>>>> -HTSLIB = "separate"
> >>>>> +HTSLIB = "external"
> >>>>> HTSLIB_DIR = []
> >>>> Thanks for the hint. For the moment it causes the build to fail
> >>> I see on the commit list that you solved the problem. Thanks !
> >> It seems to be a simple problem in setup.py. However, independently
> >> whether I activate the patch or not the tests do not work. While I
> >> checked that the symbol sam_itr_queryi is known via
> >>
> >> $ strings /usr/lib/python2.7/dist-packages/pysam/csamfile.x86_64-linux-gnu.so | grep sam_itr_queryi
> >> sam_itr_queryi
> >>
> >> I get
> >>
> >> $ python pysam_test.py
> >> Traceback (most recent call last):
> >> File "pysam_test.py", line 8, in <module>
> >> import pysam
> >> File "/usr/lib/python2.7/dist-packages/pysam/__init__.py", line 5, in <module>
> >> import pysam.csamfile as csamfile
> >> ImportError: /usr/lib/python2.7/dist-packages/pysam/csamfile.x86_64-linux-gnu.so: undefined symbol: sam_itr_queryi
> >>
> >> (same for tabix_test.py). So I guess this is no issue connected to
> >> htslib. Any idea why the tests are failing would be helpful.
> >>
> >> Kind regards
> >>
> >> Andreas.
> >>
> >> --
> >> http://fam-tille.de
> >>
> >>
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> >>
> >>
>
> --
> Olivier Sallou
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