[Bioperl-l] results of make test on bioperl-live w/ OpenBSD 3.1, Perl 5.6.1 and few dependencies installed

[chris dagdigian]

I'll tryu perl 5.8 on this platform if I can as well...

-Chris


gw# perl -v

This is perl, v5.6.1 built for i386-openbsd

####

gw# make test
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/usr/libdata/perl5/i386-openbsd/5.6.1 -I/usr/libdata/perl5 -e 'use 
Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/AAChange..........ok
t/AAReverseMutate...ok
t/AlignIO...........ok
t/AlignStats........ok
t/Allele............ok
t/Alphabet..........ok
t/Annotation........ok
t/AnnotationAdaptor.ok
t/BPbl2seq..........ok
t/BPlite............ok
t/BPpsilite.........ok
t/Biblio............SOAP::Lite not installed. Skipping some tests.
t/Biblio............ok, 1/24 skipped: unknown reason
t/BiblioReferences..ok
t/Biblio_biofetch...ok
t/BioDBGFF..........ok
t/BioFetch_DB.......ok
t/BioGraphics.......GD or Text::Shellwords modules are not installed. 
This means that Bio::Graphics module is unusable. Skipping tests.
t/BioGraphics.......ok
t/BlastIndex........ok
t/Chain.............ok
t/ClusterIO.........ok
t/CodonTable........ok
t/CoordinateMapper..ok
t/Correlate.........ok
t/CytoMap...........ok
t/DB................ok, 1/51 skipped: unknown reason
t/DBFasta...........ok
t/DNAMutation.......ok
t/ECnumber..........ok
t/EMBL_DB...........ok
t/EncodedSeq........ok
t/Exception.........ok
t/GDB...............ok
t/GFF...............ok
t/GOterm............ok
t/GeneCoordinateMapper.ok
t/Genewise..........ok
t/Genpred...........ok
t/IUPAC.............ok
t/Index.............ok
t/LinkageMap........ok
t/LiveSeq...........ok
t/LocatableSeq......ok
t/Location..........ok
t/LocationFactory...ok
t/Map...............ok
t/MapIO.............ok
t/Measure...........ok
t/MicrosatelliteMarker.ok
t/MiniMIMentry......ok
t/Molphy............ok
t/Mutation..........ok
t/Mutator...........ok
t/Node..............ok
t/OMIMentry.........ok
t/OMIMentryAllelicVariant.ok
t/OMIMparser........ok
t/OddCodes..........ok
t/PAML..............ok
t/Perl..............ok
t/Phenotype.........ok
t/PrimarySeq........ok
t/RNAChange.........ok
t/RandomTreeFactory.ok
t/Range.............ok
t/RangeI............ok
t/RefSeq............ok
t/RepeatMasker......ok
t/RestrictionEnzyme.ok
t/RootI.............ok
t/RootIO............ok
t/SearchDist........ok
t/SearchIO..........ok
t/Seq...............ok
t/SeqAnalysisParser.ok
t/SeqBuilder........ok
t/SeqDiff...........ok
t/SeqFeatCollection.ok
t/SeqFeature........ok
t/SeqIO.............ok, 3/138 skipped: unknown reason
t/SeqPattern........ok
t/SeqStats..........ok
t/SeqUtils..........ok
t/Sigcleave.........ok
t/Sim4..............ok
t/SimilarityPair....ok
t/SimpleAlign.......ok
t/Species...........ok
t/StateMachine......ok
t/StructIO..........ok
t/Structure.........ok
t/Swiss.............ok 2/5Use of uninitialized value in pattern match 
(m//) at blib/lib/Bio/SeqIO/swiss.pm line 940, <GEN2> line 13.
Use of uninitialized value in string eq at blib/lib/Bio/SeqIO/swiss.pm 
line 942, <GEN2> line 13.
t/Swiss.............ok
t/Symbol............ok
t/Tempfile..........ok
t/Term..............ok
t/Tools.............ok
t/Tree..............ok
t/TreeIO............ok
t/UniGene...........ok
t/Variation_IO......ok
t/WABA..............ok
t/XEMBL_DB..........SOAP::Lite and/or XML::DOM not installed. This means 
that Bio::DB::XEMBL module is not usable. Skipping tests.
t/XEMBL_DB..........ok
t/consed............ok
t/ePCR..............ok
t/est2genome........ok
t/flat..............ok
t/game..............ok 1/23Odd number of elements in hash assignment at 
blib/lib/Bio/Root/Root.pm line 197, <GEN0> line 88.
t/game..............ok 7/23Odd number of elements in hash assignment at 
blib/lib/Bio/Root/Root.pm line 197, <GEN1> line 88.
t/game..............ok 20/23Use of uninitialized value in pattern match 
(m//) at /usr/local/libdata/perl5/site_perl/XML/Writer.pm line 307.
Use of uninitialized value in print at 
/usr/libdata/perl5/i386-openbsd/5.6.1/IO/Handle.pm line 394.
t/game..............ok
t/hmmer.............ok
t/largefasta........Use of uninitialized value in unlink at 
blib/lib/Bio/Seq/LargePrimarySeq.pm line 287.
t/largefasta........ok 10/15Use of uninitialized value in unlink at 
blib/lib/Bio/Seq/LargePrimarySeq.pm line 287.
t/largefasta........ok 12/15Use of uninitialized value in unlink at 
blib/lib/Bio/Seq/LargePrimarySeq.pm line 287.
t/largefasta........ok
t/largepseq.........ok 5/22Use of uninitialized value in numeric lt (<) 
at blib/lib/Bio/Seq/LargePrimarySeq.pm line 194.
t/largepseq.........ok
t/lucy..............ok
t/multiple_fasta....ok
t/phd...............ok
t/primaryqual.......ok
t/primedseq.........ok
t/primer3...........ok
t/qual..............ok
t/scf...............ok
t/seqfeaturePrimer..ok
t/seqwithquality....ok
t/splicedseq........ok
t/trim..............ok 6/7Use of uninitialized value in concatenation 
(.) or string at blib/lib/Bio/Tools/Alignment/Consed.pm line 745.
Use of uninitialized value in concatenation (.) or string at 
blib/lib/Bio/Tools/Alignment/Consed.pm line 745.
t/trim..............ok
All tests successful, 5 subtests skipped.
Files=121, Tests=5044, 212 wallclock secs (108.33 cusr +  8.75 csys = 
117.08 CPU)
gw#