Re: HTSlib code copy in python-pysam.
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).
If everything is found, then it is a matter of library version not
exporting the same symbols....
>
> 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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>>
--
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