[Debian-med-packaging] Bug#846078: python-cogent: FTBFS randomly (test segfaults)

Santiago Vila sanvila at unex.es
Mon Nov 28 10:44:27 UTC 2016


Package: src:python-cogent
Version: 1.9-4
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with python2 --buildsystem=pybuild
   dh_testdir -i -O--buildsystem=pybuild
   dh_update_autotools_config -i -O--buildsystem=pybuild
   dh_auto_configure -i -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config 
warning: cogent/evolve/_solved_models.pyx:15:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cogent/evolve/_solved_models.pyx:15:33: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cogent/evolve/_solved_models.pyx:15:40: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cogent/evolve/_solved_models.pyx:15:51: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cogent/evolve/_solved_models.pyx:16:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

[... snipped ...]

copying build/lib.linux-x86_64-2.7/cogent/evolve/_likelihood_tree.so -> cogent/evolve
copying build/lib.linux-x86_64-2.7/cogent/evolve/_pairwise_distance.so -> cogent/evolve
copying build/lib.linux-x86_64-2.7/cogent/struct/_asa.so -> cogent/struct
copying build/lib.linux-x86_64-2.7/cogent/struct/_contact.so -> cogent/struct
copying build/lib.linux-x86_64-2.7/cogent/maths/_period.so -> cogent/maths
copying build/lib.linux-x86_64-2.7/cogent/maths/spatial/ckd3.so -> cogent/maths/spatial
Can't find blat executable: skipping test
Can't find carnac executable: skipping test
Can't find cmfinder.pl executable: skipping test
Can't find comrna executable: skipping test
Can't find contrafold executable: skipping test
Can't find covea executable: skipping test
Can't find dynalign executable: skipping test
Can't find FastTree executable: skipping test
Can't find foldalign executable: skipping test
Can't find guppy executable: skipping test
Can't find ilm executable: skipping test
Can't find knetfold.pl executable: skipping test
Can't find mfold executable: skipping test
Can't find msms executable: skipping test
Can't find pplacer executable: skipping test
Can't find rdp_classifier-2.2.jar executable: skipping test
Can't find rdp_classifier-2.0.jar executable: skipping test
Can't find Fold.out executable: skipping test
Can't find findphyl executable: skipping test
Can't find pknotsRG-1.2-i386-linux-static executable: skipping test
Can't find RNAalifold executable: skipping test
Can't find rnaview executable: skipping test
Can't find RNAfold executable: skipping test
Can't find sfold.X86_64.LINUX executable: skipping test
Can't find stride executable: skipping test
Can't find hybrid-ss-min executable: skipping test
Can't find calculate_likelihood executable: skipping test
Can't find sfffile executable: skipping test
Can't find sffinfo executable: skipping test
Can't find uclust executable: skipping test
Can't find usearch executable: skipping test
Environment variable TEST_DB=1 not set: skipping db tests
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
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 .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 .................................................................Segmentation fault
debian/rules:79: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 139
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:46: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------

The failure happens randomly. Sometimes it fails, sometimes it does not,
but I can reproduce the randomness on several different autobuilders.
I attach a bunch of build logs.

Thanks.
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