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

Thu Oct 2 09:10:15 UTC 2014

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
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> > > 
> > > *www.inria.fr <http://www.inria.fr/>*
> > > 
> > 
> > -- 
> > http://fam-tille.de
> > 
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