This distribution has been tested as part of the cpan-testers
effort to test as many new uploads to CPAN as possible. See
http://testers.cpan.org/
Please cc any replies to [EMAIL PROTECTED] to keep other
test volunteers informed and to prevent any duplicate effort.
--
Additional comments:
Another prerequisite (Graph.pm) that is not mentioned in Makefile.PL seems to be
causing problems. I got an out of memory error towards the end, which may also have
affected one of the test files.
--
This is an error report generated automatically by CPANPLUS,
version 0.045.
Below is the error stack during 'make' & 'make test':
Writing Makefile for Bio::Das
Warning: prerequisite Bio::Root::Root 0 not found.
Do you want to run the BioDBGFF tests (requires a mysql database) y/n [n] n
External Module Text::Shellwords, Execute shell commands,
is not installed on this computer.
The Bio::Graphics in Bioperl needs it for test scripts
External Module Ace, Aceperl,
is not installed on this computer.
The Bio::DB::Ace in Bioperl needs it for access of ACeDB database
External Module XML::Parser::PerlSAX, Parsing of XML documents,
is not installed on this computer.
The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation code,
GAME parser
External Module XML::Writer, Parsing + writing of XML documents,
is not installed on this computer.
The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation code,
GAME parser
External Module Graph::Directed, Generic Graph data stucture and algorithms,
is not installed on this computer.
The Bio::Ontology::SimpleOntologyEngine in Bioperl needs it for Ontology Engine
implementation for the GO parser
Information:
There are some external packages and perl modules, listed above, which
bioperl uses. This only effects the functionality which is listed above:
the rest of bioperl will work fine, which includes nearly all of the
core packages.
The installation of these external packages is very simple. You
can read more about bioperl external dependencies at
http://bioperl.org/Core/external.shtml
Enjoy the rest of bioperl, which you can use after going 'make install'
Writing Makefile for Bio
Generated sub tests. go make show_tests to see available subtests
C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0,
'blib\lib', 'blib\arch')" t\AAChange.t t\AAReverseMutate.t t\AlignIO.t t\AlignStats.t
t\Allele.t t\Alphabet.t t\Annotation.t t\AnnotationAdaptor.t t\Assembly.t t\Biblio.t
t\Biblio_biofetch.t t\BiblioReferences.t t\BioDBGFF.t t\BioFetch_DB.t t\BioGraphics.t
t\BlastIndex.t t\BPbl2seq.t t\BPlite.t t\BPpsilite.t t\Chain.t t\ClusterIO.t
t\CodonTable.t t\consed.t t\CoordinateGraph.t t\CoordinateMapper.t t\Correlate.t
t\CytoMap.t t\DB.t t\DBFasta.t t\DNAMutation.t t\ECnumber.t t\EMBL_DB.t t\EncodedSeq.t
t\ePCR.t t\est2genome.t t\Exception.t t\Exonerate.t t\flat.t t\FootPrinter.t t\game.t
t\GDB.t t\GeneCoordinateMapper.t t\Genewise.t t\Genomewise.t t\Genpred.t t\GFF.t
t\GOterm.t t\hmmer.t t\Index.t t\IUPAC.t t\largefasta.t t\largepseq.t t\LinkageMap.t
t\LiveSeq.t t\LocatableSeq.t t\Location.t t\LocationFactory.t t\LocusLink.t t\lucy.t
t\Map.t t\MapIO.t t\Measure.t t\MicrosatelliteMarker.t t\MiniMIMentry.t t\Molphy.t
t\multiple_fasta.t t\Mutation.t t\Mutator.t t\Node.t t\OddCodes.t t\OMIMentry.t
t\OMIMentryAllelicVariant.t t\OMIMparser.t t\Ontology.t t\OntologyEngine.t t\PAML.t
t\Perl.t t\phd.t t\Phenotype.t t\PhylipDist.t t\primaryqual.t t\PrimarySeq.t
t\primedseq.t t\primer3.t t\ProtDist.t t\qual.t t\RandomTreeFactory.t t\Range.t
t\RangeI.t t\RefSeq.t t\Relationship.t t\RelationshipType.t t\RepeatMasker.t
t\RestrictionEnzyme.t t\RNAChange.t t\RootI.t t\RootIO.t t\scf.t t\SearchDist.t
t\SearchIO.t t\Seq.t t\SeqAnalysisParser.t t\SeqBuilder.t t\SeqDiff.t
t\SeqFeatCollection.t t\SeqFeature.t t\seqfeaturePrimer.t t\SeqIO.t t\SeqPattern.t
t\SeqStats.t t\SequenceFamily.t t\sequencetrace.t t\SeqUtils.t t\seqwithquality.t
t\Sigcleave.t t\Sim4.t t\SimilarityPair.t t\SimpleAlign.t t\simpleGOparser.t
t\Species.t t\splicedseq.t t\StandAloneBlast.t t\StateMachine.t t\StructIO.t
t\Structure.t t\Swiss.t t\Symbol.t t\Tempfile.t t\Term.t t\Tools.t t\Tree.t t\TreeIO.t
t\trim.t t\UniGene.t t\Variation_IO.t t\WABA.t t\XEMBL_DB.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\Assembly...................ok
t\Biblio.....................ok
t\Biblio_biofetch............ok
t\BiblioReferences...........ok
t\BioDBGFF...................ok
t\BioFetch_DB................ok
t\BioGraphics................ok
t\BlastIndex.................ok
t\BPbl2seq...................ok
t\BPlite.....................ok
t\BPpsilite..................ok
t\Chain......................ok
t\ClusterIO..................ok
t\CodonTable.................ok
t\consed.....................ok
t\CoordinateGraph............ok
t\CoordinateMapper...........ok
t\Correlate..................ok
t\CytoMap....................ok
t\DB.........................FAILED tests 67-69
Failed 3/78 tests, 96.15% okay (less 1 skipped test: 74 okay, 94.87%)
t\DBFasta....................ok
t\DNAMutation................ok
t\ECnumber...................ok
t\EMBL_DB....................ok
t\EncodedSeq.................ok
t\ePCR.......................ok
t\est2genome.................ok
t\Exception..................ok
t\Exonerate..................ok
t\flat.......................ok
t\FootPrinter................ok
t\game.......................ok
t\GDB........................ok
t\GeneCoordinateMapper.......ok
t\Genewise...................ok
t\Genomewise.................ok
t\Genpred....................ok
t\GFF........................ok
t\GOterm.....................ok
t\hmmer......................ok
t\Index......................dubious
Test returned status 2 (wstat 512, 0x200)
after all the subtests completed successfully
t\IUPAC......................ok
t\largefasta.................ok
t\largepseq..................ok
t\LinkageMap.................ok
t\LiveSeq....................ok
t\LocatableSeq...............ok
t\Location...................ok
t\LocationFactory............ok
t\LocusLink..................ok
t\lucy.......................ok
t\Map........................ok
t\MapIO......................ok
t\Measure....................ok
t\MicrosatelliteMarker.......ok
t\MiniMIMentry...............ok
t\Molphy.....................ok
t\multiple_fasta.............ok
t\Mutation...................ok
t\Mutator....................ok
t\Node.......................ok
t\OddCodes...................ok
t\OMIMentry..................ok
t\OMIMentryAllelicVariant....ok
t\OMIMparser.................ok
t\Ontology...................ok
t\OntologyEngine.............ok
t\PAML.......................ok
t\Perl.......................ok
t\phd........................ok
t\Phenotype..................ok
t\PhylipDist.................ok
t\primaryqual................ok
t\PrimarySeq.................ok
t\primedseq..................ok
t\primer3....................ok
t\ProtDist...................ok
t\qual.......................ok
t\RandomTreeFactory..........ok
t\Range......................ok
t\RangeI.....................ok
t\RefSeq.....................ok
t\Relationship...............ok
t\RelationshipType...........ok
t\RepeatMasker...............ok
t\RestrictionEnzyme..........ok
t\RNAChange..................ok
t\RootI......................ok
t\RootIO.....................ok
t\scf........................dubious
Test returned status 1 (wstat 256, 0x100)
DIED. FAILED tests 2-15
Failed 14/15 tests, 6.67% okay
t\SearchDist.................ok
t\SearchIO...................ok
t\Seq........................ok
t\SeqAnalysisParser..........ok
t\SeqBuilder.................ok
t\SeqDiff....................ok
t\SeqFeatCollection..........dubious
Test returned status 13 (wstat 3328, 0xd00)
DIED. FAILED tests 12-428
Failed 417/428 tests, 2.57% okay
t\SeqFeature.................ok
t\seqfeaturePrimer...........ok
t\SeqIO......................ok
3/184 skipped:
t\SeqPattern.................ok
t\SeqStats...................ok
t\SequenceFamily.............ok
t\sequencetrace..............ok
t\SeqUtils...................ok
t\seqwithquality.............ok
t\Sigcleave..................ok
t\Sim4.......................ok
t\SimilarityPair.............ok
t\SimpleAlign................ok
t\simpleGOparser.............ok
t\Species....................ok
t\splicedseq.................ok
t\StandAloneBlast............ok
t\StateMachine...............ok
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t\DB.t 78 3 3.85% 67-69
t\Index.t 2 512 32 0 0.00% ??
t\SeqFeatCollection.t 13 3328 428 834 194.86% 12-428
t\scf.t 1 256 15 28 186.67% 2-15
4 subtests skipped.
Microsoft (R) Program Maintenance Utility Version 1.50
Copyright (c) Microsoft Corp 1988-94. All rights reserved.
GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module
is unusable. Skipping tests.
XML::Parser::PerlSAX not loaded. This means ClusterIO::dbsnp test cannot be executed.
Skipping
XML::Parser::PerlSAX not loaded. This means game test cannot be executed. Skipping
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: File does not exist
'\cygdrive\c\.cpanplus\5.6.1\build\bioperl-1.2.3\t\data\multifa.seq'
STACK: Error::throw
STACK: Bio::Root::Root::throw
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio/Root/Root.pm:342
STACK: Bio::Index::Abstract::make_index
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio/Index/Abstract.pm:568
STACK: t\Index.t:52
-----------------------------------------------------------
Subroutine new redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 93, <GEN0> line
6.
Subroutine nodelete redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 120, <GEN0> line
6.
Subroutine get_nodes redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 137, <GEN0> line
6.
Subroutine get_root_node redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 173, <GEN0> line
6.
Subroutine set_root_node redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 188, <GEN0> line
6.
Subroutine total_branch_length redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 212, <GEN0> line
6.
Subroutine id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 234, <GEN0> line
6.
Subroutine score redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 255, <GEN0> line
6.
Subroutine cleanup_tree redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 292, <GEN0> line
6.
Subroutine new redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 100, <GEN0> line
6.
Subroutine add_Descendent redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 152, <GEN0> line
6.
Subroutine each_Descendent redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 185, <GEN0> line
6.
Subroutine remove_Descendent redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 221, <GEN0> line
6.
Subroutine remove_all_Descendents redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 268, <GEN0> line
6.
Subroutine ancestor redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 302, <GEN0> line
6.
Subroutine branch_length redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 319, <GEN0> line
6.
Subroutine bootstrap redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 344, <GEN0> line
6.
Subroutine description redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 366, <GEN0> line
6.
Subroutine id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 391, <GEN0> line
6.
Subroutine internal_id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 415, <GEN0> line
6.
Subroutine _creation_id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 431, <GEN0> line
6.
Subroutine is_Leaf redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 452, <GEN0> line
6.
Subroutine height redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 478, <GEN0> line
6.
Subroutine invalidate_height redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 511, <GEN0> line
6.
Subroutine add_tag_value redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 532, <GEN0> line
6.
Subroutine remove_tag redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 552, <GEN0> line
6.
Subroutine remove_all_tags redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 573, <GEN0> line
6.
Subroutine get_all_tags redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 590, <GEN0> line
6.
Subroutine get_tag_values redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 606, <GEN0> line
6.
Subroutine has_tag redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 622, <GEN0> line
6.
Subroutine node_cleanup redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 627, <GEN0> line
6.
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...
Subroutine new redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 132.
Subroutine init redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 183.
Subroutine identifier redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 208.
Subroutine subject_term redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 238.
Subroutine object_term redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 269.
Subroutine predicate_term redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 300.
Subroutine ontology redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 325.
Subroutine to_string redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 353.
Subroutine _check_class redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 375.
Subroutine child_term redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 401.
Subroutine parent_term redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 402.
Subroutine relationship_type redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Ontology\Relationship.pm line 403.
Subroutine _initialize redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\phd.pm line 72.
Subroutine next_seq redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\phd.pm line 95.
Subroutine write_seq redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\phd.pm line 171.
Subroutine _initialize redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\qual.pm line 76.
Subroutine next_seq redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\qual.pm line 96.
Subroutine _next_qual redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\qual.pm line 138.
Subroutine next_primary_qual redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\qual.pm line 153.
Subroutine write_seq redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\qual.pm line 202.
Subroutine new redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 93.
Subroutine nodelete redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 120.
Subroutine get_nodes redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 137.
Subroutine get_root_node redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 173.
Subroutine set_root_node redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 188.
Subroutine total_branch_length redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 212.
Subroutine id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 234.
Subroutine score redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 255.
Subroutine cleanup_tree redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Tree.pm line 292.
Subroutine new redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 100.
Subroutine add_Descendent redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 152.
Subroutine each_Descendent redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 185.
Subroutine remove_Descendent redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 221.
Subroutine remove_all_Descendents redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 268.
Subroutine ancestor redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 302.
Subroutine branch_length redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 319.
Subroutine bootstrap redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 344.
Subroutine description redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 366.
Subroutine id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 391.
Subroutine internal_id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 415.
Subroutine _creation_id redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 431.
Subroutine is_Leaf redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 452.
Subroutine height redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 478.
Subroutine invalidate_height redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 511.
Subroutine add_tag_value redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 532.
Subroutine remove_tag redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 552.
Subroutine remove_all_tags redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 573.
Subroutine get_all_tags redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 590.
Subroutine get_tag_values redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 606.
Subroutine has_tag redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 622.
Subroutine node_cleanup redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\Tree\Node.pm line 627.
sleeping for 3 seconds
Subroutine _initialize redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 82.
Subroutine next_seq redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 109.
Subroutine _set_v3_quality redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 215.
Subroutine _set_v3_peak_indices redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 242.
Subroutine _set_v3_base_accuracies redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 262.
Subroutine _set_comments redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 293.
Subroutine _set_header redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 324.
Subroutine _set_v2_bases redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 357.
Subroutine _set_v2_traces redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 394.
Subroutine get_trace redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 426.
Subroutine get_peak_indices redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 448.
Subroutine get_header redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 466.
Subroutine _dump_traces_incoming redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 493.
Subroutine _dump_traces_outgoing redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 526.
Subroutine write_seq redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 574.
Subroutine _set_binary_header redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 721.
Subroutine _set_binary_tracesbases redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 756.
Subroutine _make_trace_string redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 936.
Subroutine _set_binary_comments redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 978.
Subroutine _fill_missing_data redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1008.
Subroutine _delta redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1037.
Subroutine _unpack_magik redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1099.
Subroutine read_from_buffer redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1124.
Subroutine _dump_keys redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1152.
Subroutine _dump_base_accuracies redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1175.
Subroutine _dump_peak_indices_incoming redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1202.
Subroutine _dump_base_accuracies_incoming redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1223.
Subroutine _dump_comments redefined at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio\SeqIO\scf.pm line 1250.
Out of memory!
XML::Parser::PerlSAX or HTML::Entities not loaded. This means SearchIO::blastxml test
cannot be executed. Skipping
Subroutine new redefined at Bio/Search/HSP/GenericHSP.pm line 148, <GEN5> line 353.
Subroutine algorithm redefined at Bio/Search/HSP/GenericHSP.pm line 346, <GEN5> line
353.
Subroutine pvalue redefined at Bio/Search/HSP/GenericHSP.pm line 368, <GEN5> line 353.
Subroutine evalue redefined at Bio/Search/HSP/GenericHSP.pm line 387, <GEN5> line 353.
Subroutine frac_identical redefined at Bio/Search/HSP/GenericHSP.pm line 403, <GEN5>
line 353.
Subroutine frac_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 437, <GEN5>
line 353.
Subroutine gaps redefined at Bio/Search/HSP/GenericHSP.pm line 464, <GEN5> line 353.
Subroutine query_string redefined at Bio/Search/HSP/GenericHSP.pm line 489, <GEN5>
line 353.
Subroutine hit_string redefined at Bio/Search/HSP/GenericHSP.pm line 513, <GEN5> line
353.
Subroutine homology_string redefined at Bio/Search/HSP/GenericHSP.pm line 539, <GEN5>
line 353.
Subroutine length redefined at Bio/Search/HSP/GenericHSP.pm line 569, <GEN5> line 353.
Subroutine hsp_length redefined at Bio/Search/HSP/GenericHSP.pm line 601, <GEN5> line
353.
Subroutine frame redefined at Bio/Search/HSP/GenericHSP.pm line 632, <GEN5> line 353.
Subroutine get_aln redefined at Bio/Search/HSP/GenericHSP.pm line 700, <GEN5> line 353.
Subroutine num_conserved redefined at Bio/Search/HSP/GenericHSP.pm line 746, <GEN5>
line 353.
Subroutine num_identical redefined at Bio/Search/HSP/GenericHSP.pm line 765, <GEN5>
line 353.
Subroutine rank redefined at Bio/Search/HSP/GenericHSP.pm line 783, <GEN5> line 353.
Subroutine seq_inds redefined at Bio/Search/HSP/GenericHSP.pm line 821, <GEN5> line
353.
Subroutine score redefined at Bio/Search/HSP/GenericHSP.pm line 933, <GEN5> line 353.
Subroutine bits redefined at Bio/Search/HSP/GenericHSP.pm line 954, <GEN5> line 353.
Subroutine _calculate_seq_positions redefined at Bio/Search/HSP/GenericHSP.pm line
990, <GEN5> line 353.
Subroutine n redefined at Bio/Search/HSP/GenericHSP.pm line 1092, <GEN5> line 353.
Subroutine range redefined at Bio/Search/HSP/GenericHSP.pm line 1105, <GEN5> line 353.
Can't call method "get_dup" on an undefined value at
C:\.cpanplus\5.6.1\build\bioperl-1.2.3\blib\lib/Bio/SeqFeature/Collection.pm line 297.
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...
Failed 4/123 test scripts, 96.75% okay. 434/5841 subtests failed, 92.57% okay.
NMAKE : fatal error U1077: 'C:\WINNT\system32\cmd.exe' : return code '0xff'
Stop.
--
Summary of my perl5 (revision 5 version 6 subversion 1) configuration:
Platform:
osname=MSWin32, osvers=4.0, archname=MSWin32-x86-multi-thread
uname=''
config_args='undef'
hint=recommended, useposix=true, d_sigaction=undef
usethreads=undef use5005threads=undef useithreads=define usemultiplicity=define
useperlio=undef d_sfio=undef uselargefiles=undef usesocks=undef
use64bitint=undef use64bitall=undef uselongdouble=undef
Compiler:
cc='cl', ccflags ='-nologo -O1 -MD -Zi -DNDEBUG -DWIN32 -D_CONSOLE -DNO_STRICT
-DHAVE_DES_FCRYPT -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DPERL_MSVCRT_READFIX',
optimize='-O1 -MD -Zi -DNDEBUG',
cppflags='-DWIN32'
ccversion='', gccversion='', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=undef, longlongsize=8, d_longdbl=define, longdblsize=10
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=4
alignbytes=8, usemymalloc=n, prototype=define
Linker and Libraries:
ld='link', ldflags ='-nologo -nodefaultlib -debug -opt:ref,icf
-libpath:"C:\Perl\lib\CORE" -machine:x86'
libpth="C:\Perl\lib\CORE"
libs= oldnames.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib
advapi32.lib shell32.lib ole32.lib oleaut32.lib netapi32.lib uuid.lib wsock32.lib
mpr.lib winmm.lib version.lib odbc32.lib odbccp32.lib msvcrt.lib
perllibs= oldnames.lib kernel32.lib user32.lib gdi32.lib winspool.lib
comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib netapi32.lib uuid.lib
wsock32.lib mpr.lib winmm.lib version.lib odbc32.lib odbccp32.lib msvcrt.lib
libc=msvcrt.lib, so=dll, useshrplib=yes, libperl=perl56.lib
Dynamic Linking:
dlsrc=dl_win32.xs, dlext=dll, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-dll -nologo -nodefaultlib -debug -opt:ref,icf
-libpath:"C:\Perl\lib\CORE" -machine:x86'
