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

[Andreas Tille]

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
> >
> 
> 
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