Re: HTSlib code copy in python-pysam.
On 08/25/2014 04:37 PM, Andreas Tille wrote:
> 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?
code would need to be modified to use the new lib API, but this can be
quite hard depending on modifications.... and difficult to detect where
in the code this API differs... :-(
>
> 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
>> IRISA / University of Rennes 1
>> Campus de Beaulieu, 35000 RENNES - FRANCE
>> Tel: 02.99.84.71.95
>>
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>>
>>
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>>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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