[Bioperl-l] 'make test' results for bioperl-live on Solaris 8 w/ perl 5.6.1 and
few dependencies
Chris Dagdigian
dag@sonsorol.org
Sat, 12 Oct 2002 13:18:30 -0400
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#
# uname -a
SunOS cvs 5.8 Generic_108528-16 sun4u sparc SUNW,UltraAX-i2
#
# /usr/local/bin/perl -v
This is perl, v5.6.1 built for sun4-solaris
Copyright 1987-2001, Larry Wall
Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using `man perl' or `perldoc perl'. If you have access to the
Internet, point your browser at http://www.perl.com/, the Perl Home Page.
# make test
PERL_DL_NONLAZY=1 /usr/local/bin/perl -Iblib/arch -Iblib/lib -I/usr/local/lib/perl5/5.6.1/sun4-solaris -I/usr/local/lib/perl5/5.6.1 -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.
IO::String not installed. Skipping some tests.
XML::Parser not installed. Skipping some tests.
t/Biblio.....................ok
22/24 skipped:
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..................XML::Parser::PerlSAX not loaded. This means ClusterIO::dbsnp test cannot be executed. Skipping
t/ClusterIO..................ok
t/CodonTable.................ok
t/CoordinateMapper...........ok
t/Correlate..................ok
t/CytoMap....................ok
t/DB.........................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests.
t/DB.........................ok
t/DBFasta....................AnyDBM_File doesn't define an EXISTS method at Bio/DB/Fasta.pm line 789
indexing was interrupted, so unlinking ./t/data/dbfa/directory.index at Bio/DB/Fasta.pm line 948.
t/DBFasta....................dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-11
Failed 11/11 tests, 0.00% okay
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......................FAILED tests 1, 4-5, 7, 9
Failed 5/12 tests, 58.33% okay
t/LinkageMap.................ok
t/LiveSeq....................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests.
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.....................no IO string installed
t/Molphy.....................ok
t/Mutation...................ok
t/Mutator....................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests.
t/Mutator....................ok
t/Node.......................ok
t/OMIMentry..................ok
t/OMIMentryAllelicVariant....ok
t/OMIMparser.................ok
t/OddCodes...................ok
t/PAML.......................no IO string installed
t/PAML.......................ok
t/Perl.......................IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping some tests.
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...................XML::Parser::PerlSAX not loaded. This means SearchIO::blastxml test cannot be executed. Skipping
t/SearchIO...................ok
t/Seq........................ok
t/SeqAnalysisParser..........ok
t/SeqBuilder.................ok
t/SeqDiff....................ok
t/SeqFeatCollection..........Can't locate DB_File.pm in @INC (@INC contains: t blib/arch blib/lib /usr/local/lib/perl5/5.6.1/sun4-solaris /usr/local/lib/perl5/5.6.1 /usr/local/lib/perl5/site_perl/5.6.1/sun4-solaris /usr/local/lib/perl5/site_perl/5.6.1 /usr/local/lib/perl5/site_perl .) at blib/lib/Bio/SeqFeature/Collection.pm line 121.
BEGIN failed--compilation aborted at blib/lib/Bio/SeqFeature/Collection.pm line 121.
Compilation failed in require at t/SeqFeatCollection.t line 43.
BEGIN failed--compilation aborted at t/SeqFeatCollection.t line 43.
t/SeqFeatCollection..........dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-12
Failed 12/12 tests, 0.00% okay
t/SeqFeature.................ok
t/SeqIO......................ok
3/138 skipped:
t/SeqPattern.................ok
t/SeqStats...................ok
t/SeqUtils...................ok
t/Sigcleave..................ok
t/Sim4.......................ok
t/SimilarityPair.............ok
t/SimpleAlign................ok 48/55IO::String not installed. Skipping tests.
t/SimpleAlign................ok
t/Species....................ok
t/StateMachine...............ok
t/StructIO...................ok
t/Structure..................ok
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 10/25
The XML-format conversion requires the CPAN modules XML::Twig, XML::Writer, and IO::String to be installed on your system, which they probably aren't. Skipping these tests.
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.......................DB_File not loaded. This means flat.t test cannot be executed. Skipping
t/flat.......................ok 7/7No root path(s) specified
at blib/lib/Bio/Root/IO.pm line 754
t/flat.......................ok
t/game.......................XML::Parser::PerlSAX not loaded. This means game test cannot be executed. Skipping
t/game.......................ok
t/hmmer......................ok
t/largefasta.................ok
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 9/9Skipping remote location tests
t/splicedseq.................ok
t/trim.......................ok
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t/DBFasta.t 2 512 11 11 100.00% 1-11
t/Index.t 12 5 41.67% 1 4-5 7 9
t/SeqFeatCollection.t 2 512 12 12 100.00% 1-12
25 subtests skipped.
Failed 3/121 test scripts, 97.52% okay. 28/5044 subtests failed, 99.44% okay.
*** Error code 11
make: Fatal error: Command failed for target `test_dynamic'
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