[Debian-med-packaging] kissplice test fails on several architectures

David Parsons david.parsons at inria.fr
Thu Oct 2 09:46:26 UTC 2014


Hi Andreas,

Sorry I hadn't seen your previous mail.
I'll try to get an answer and apply the changes ASAP

Thank you,
David


On 02/10/2014 11:10, Andreas Tille wrote:
> Hi David,
>
> I forgot to CC you in my last ping.  Please note that it is evident to
> react *right now* if you want to get the latest version into the next
> stable release.
>
> Kind regards
>
>           Andreas.
>
> On Tue, Sep 30, 2014 at 04:10:07PM +0200, Andreas Tille wrote:
>> Hi David,
>>
>> any news about this?
>>
>> Kind regards
>>
>>         Andreas.
>>
>> On Wed, Sep 17, 2014 at 03:21:43PM +0200, Andreas Tille wrote:
>>> Hi David,
>>>
>>> On Tue, Sep 16, 2014 at 05:07:21PM +0200, David Parsons wrote:
>>>> Hi Andreas,
>>>>
>>>> I remember the kissplice team decided to stop maintaining for non
>>>> 64bit architectures. So I suppose this is it.
>>>> I will ask them what they think but I guess they will choose to
>>>> simply restrain the package to 64bit archs. Would that be OK in
>>>> debian-med standards ?
>>> Yes, for sure.  It just needs to be expressed in debian/control
>>> accordingly.  So please let us know to be sure and than upload a
>>> proper package.
>>>
>>>> Thanks for the input,
>>> You are welcome
>>>
>>>         Andreas.
>>>   
>>>> On 16/09/2014 16:51, Andreas Tille wrote:
>>>>> Hi David,
>>>>>
>>>>> according to the build status page of kissplice[1] the tests are failing
>>>>> on non 64bit architectures.  Using the log of i386 as example it looks
>>>>> like
>>>>>
>>>>> ...
>>>>>     dh_auto_test -a
>>>>> make[1]: Entering directory '/«PKGBUILDDIR»/obj-i586-linux-gnu'
>>>>> Running tests...
>>>>> /usr/bin/ctest --force-new-ctest-process -j1
>>>>> Test project /«PKGBUILDDIR»/obj-i586-linux-gnu
>>>>>      Start 1: KisspliceBasicTest
>>>>> 1/8 Test #1: KisspliceBasicTest ...............   Passed    0.11 sec
>>>>>      Start 2: KisspliceDBGTest
>>>>> 2/8 Test #2: KisspliceDBGTest .................***Failed  Required regular expression not found.Regex=[test SUCCESSFUL
>>>>> ] 30.98 sec
>>>>> /«PKGBUILDDIR»/obj-i586-linux-gnu/bin/kissplice -k 25 -M 1000 -r /«PKGBUILDDIR»/tests/integration_tests/data/HBM75brain_100000.fasta -r /«PKGBUILDDIR»/tests/integration_tests/data/HBM75liver_100000.fasta -o /«PKGBUILDDIR»/tests/integration_tests/results
>>>>> Integration test error :  Problem with /«PKGBUILDDIR»/obj-i586-linux-gnu/lib/kissplice/ks_kissreadsSNPS
>>>>>
>>>>>
>>>>>      Start 3: KisspliceTwoSequencesTest
>>>>> 3/8 Test #3: KisspliceTwoSequencesTest ........***Failed  Required regular expression not found.Regex=[test SUCCESSFUL
>>>>> ] 21.68 sec
>>>>> /«PKGBUILDDIR»/obj-i586-linux-gnu/bin/kissplice -s -k 25 -M 1000 -r /«PKGBUILDDIR»/tests/integration_tests/data/HBM75brain_100000.fasta -r /«PKGBUILDDIR»/tests/integration_tests/data/HBM75liver_100000.fasta -C 0
>>>>> Integration test error :  Problem with /«PKGBUILDDIR»/obj-i586-linux-gnu/lib/kissplice/ks_kissreadsSNPS
>>>>>
>>>>>
>>>>>      Start 4: KisspliceGraphAndSequenceTest
>>>>> 4/8 Test #4: KisspliceGraphAndSequenceTest ....***Failed  Required regular expression not found.Regex=[test SUCCESSFUL
>>>>> ] 10.03 sec
>>>>> /«PKGBUILDDIR»/obj-i586-linux-gnu/bin/kissplice -s -k 25 -M 1000 -g /«PKGBUILDDIR»/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /«PKGBUILDDIR»/tests/integration_tests/data/HBM75brain_100000.fasta -C 0
>>>>> Integration test error :  Problem with /«PKGBUILDDIR»/obj-i586-linux-gnu/lib/kissplice/ks_kissreadsSNPS
>>>>>
>>>>>
>>>>>      Start 5: KisspliceGraphTest
>>>>> 5/8 Test #5: KisspliceGraphTest ...............   Passed   10.04 sec
>>>>>      Start 6: ksBubbleEnumerationTest
>>>>> 6/8 Test #6: ksBubbleEnumerationTest ..........   Passed    0.04 sec
>>>>>      Start 7: ksRunModulesTest
>>>>> 7/8 Test #7: ksRunModulesTest .................   Passed    0.05 sec
>>>>>      Start 8: ksErrorRemovalTest
>>>>> 8/8 Test #8: ksErrorRemovalTest ...............   Passed    0.13 sec
>>>>>
>>>>> 63% tests passed, 3 tests failed out of 8
>>>>>
>>>>> Total Test time (real) =  73.08 sec
>>>>>
>>>>> The following tests FAILED:
>>>>> 	  2 - KisspliceDBGTest (Failed)
>>>>> 	  3 - KisspliceTwoSequencesTest (Failed)
>>>>> 	  4 - KisspliceGraphAndSequenceTest (Failed)
>>>>> Errors while running CTest
>>>>> make[1]: *** [test] Error 8
>>>>> ...
>>>>>
>>>>>
>>>>> Do you see any chance to fix this?
>>>>>
>>>>> Kind regards
>>>>>
>>>>>         Andreas.
>>>>>
>>>>>
>>>>> [1] https://buildd.debian.org/status/package.php?p=kissplice
>>>>>
>>>>
>>>> -- 
>>>> Untitled
>>>>
>>>>
>>>> logo
>>>>
>>>>
>>>> *David Parsons* <http://www.parsons.eu/>
>>>> Service d'Expérimentation et de Développement
>>>>
>>>> Antenne Inria Lyon - La Doua
>>>> Bâtiment CEI-2
>>>> 56 Boulevard Niels Bohr
>>>> CS 52132
>>>> 69603 Villeurbanne
>>>> Tel : +33 (0)4 72 43 74 97
>>>>
>>>> *www.inria.fr <http://www.inria.fr/>*
>>>>
>>> -- 
>>> http://fam-tille.de
>>>
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>>
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-- 
Untitled


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*David Parsons* <http://www.parsons.eu/>
Service d'Expérimentation et de Développement

Antenne Inria Lyon - La Doua
Bâtiment CEI-2
56 Boulevard Niels Bohr
CS 52132
69603 Villeurbanne
Tel : +33 (0)4 72 43 74 97

*www.inria.fr <http://www.inria.fr/>*

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