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

Fri Oct 10 08:31:43 UTC 2014

Hi Andreas,

I gave it a try and just pushed a minute ago.
Hope it finds its way through
If not, I'm afraid it will have to wait for at least Wednesday...

David

On 10/10/2014 09:48, Andreas Tille wrote:
> Hi David,
>
> sorry to ping again.  To make things clear:  Either we are very quick
> with editing the control file according to the architecture where it
> builds or Debian will ship in its next stable release with an older
> version.  There is not much time left until freeze.  It is fine if you
> would express:  "I have no time - please can anybody else adapt the
> debian/control file."
>
> Kind regards
>
>          Andreas.
>
> On Thu, Oct 02, 2014 at 11:10:15AM +0200, 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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-- 
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

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