[Bioperl-l] Failed tests for FeatureIO

Chris Fields cjfields at uiuc.edu
Mon Sep 25 00:50:20 EDT 2006


I am getting failed tests for FeatureIO.t on make test using bioperl- 
live on Mac OS X (10.4.7, perl 5.8.6):

Failed Test   Stat Wstat Total Fail  List of Failed
------------------------------------------------------------------------ 
-------
t/FeatureIO.t  255 65280    33    0  ??
5 subtests skipped.
Failed 1/238 test scripts. 0/12392 subtests failed.
Files=238, Tests=12392, 402 wallclock secs (99.35 cusr + 14.14 csys =  
113.49 CPU)
Failed 1/238 test programs. 0/12392 subtests failed.


Here's the direct run:

pyr:~/src/bioperl-live cjfields$ perl -I. -w t/FeatureIO.t
1..33
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15

-------------------- WARNING ---------------------
MSG: '##feature-ontology' directive handling not yet implemented
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: '##attribute-ontology' directive handling not yet implemented
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: '##source-ontology' directive handling not yet implemented
---------------------------------------------------
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Invalid protein count
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:331
STACK: Bio::FeatureIO::ptt::_initialize Bio/FeatureIO/ptt.pm:147
STACK: Bio::FeatureIO::new Bio/FeatureIO.pm:266
STACK: Bio::FeatureIO::new Bio/FeatureIO.pm:286
STACK: t/FeatureIO.t:189
-----------------------------------------------------------
ok 23 # Cannot complete FeatureIO tests
ok 24 # Cannot complete FeatureIO tests
ok 25 # Cannot complete FeatureIO tests
ok 26 # Cannot complete FeatureIO tests
ok 27 # Cannot complete FeatureIO tests
ok 28 # Cannot complete FeatureIO tests
ok 29 # Cannot complete FeatureIO tests
ok 30 # Cannot complete FeatureIO tests
ok 31 # Cannot complete FeatureIO tests
ok 32 # Cannot complete FeatureIO tests
ok 33 # Cannot complete FeatureIO tests


Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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