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FAIL bioperl-1.4 i686-linux-thread-multi-64int 2.6.22-1-k7
From:
andreas.koenig.gmwojprw
Date:
April 17, 2008 12:37
Subject:
FAIL bioperl-1.4 i686-linux-thread-multi-64int 2.6.22-1-k7
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/
--
Dear Ewan Birney,
This is a computer-generated report for bioperl-1.4
on perl 5.10.0 patch 33412, created by CPAN-Reporter-1.1402.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://cpantest.grango.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 /home/src/perl/repoperls/installed-perls/maint-5.10/piB7lpk/perl-5.10.0@33412/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/AAChange.....................ok
t/AAReverseMutate..............ok
t/AlignIO......................ok
t/AlignStats...................ok
t/Allele.......................ok
t/Alphabet.....................ok
t/Annotation...................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/AnnotationAdaptor............ok
t/Assembly.....................ok
t/Biblio.......................ok
t/Biblio_biofetch..............ok
t/BiblioReferences.............ok
t/BioDBGFF.....................ok
t/BioFetch_DB.................. Failed 3/27 subtests
t/BioGraphics..................ok
t/BlastIndex...................ok
t/BPbl2seq.....................ok
t/BPlite.......................ok
t/BPpsilite....................ok
t/Chain........................ok
t/cigarstring..................ok
t/ClusterIO....................ok
t/Coalescent...................ok
t/CodonTable...................ok
t/consed.......................ok
t/CoordinateGraph..............ok
t/CoordinateMapper.............ok
t/Correlate....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/CytoMap......................ok
t/DB........................... Failed 2/78 subtests
(less 1 skipped subtest: 75 okay)
t/DBCUTG.......................ok
t/DBFasta......................ok
t/DNAMutation..................ok
t/Domcut.......................ok
t/ECnumber.....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/ELM..........................
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 URL must be absolute
Content-Type: text/plain
Client-Date: Thu, 17 Apr 2008 19:34:46 GMT
Client-Warning: Internal response
400 URL must be absolute
---------------------------------------------------
ok
t/EMBL_DB...................... Failed 3/15 subtests
t/EMBOSS_Tools.................ok
t/EncodedSeq...................ok
t/ePCR.........................ok
t/ESEfinder....................ok
t/est2genome...................ok
t/Exception....................ok
t/Exonerate....................ok
t/flat.........................ok
t/FootPrinter..................ok
t/game.........................ok
t/GDB..........................ok
t/GeneCoordinateMapper.........
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
ok
t/Geneid.......................ok
t/Genewise.....................ok
t/Genomewise...................ok
t/Genpred......................ok
t/GFF..........................Filehandle GEN0 opened only for output at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/IO.pm line 440.
ok
t/GOR4.........................ok
t/GOterm.......................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/GuessSeqFormat...............ok
t/hmmer........................ok
t/HNN..........................ok
t/Index........................ok
t/InstanceSite.................ok
t/InterProParser...............Useless localization of scalar assignment at Bio/Root/Object.pm line 699.
ok
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....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/lucy.........................ok
t/Map..........................ok
t/MapIO........................ok
t/Matrix.......................ok
t/Measure......................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/MeSH.........................Use of uninitialized value $desc in substitution (s///) at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/DB/MeSH.pm line 263.
Use of uninitialized value $name in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value $name in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value $name in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/DB/MeSH.pm line 277.
Failed 1/26 subtests
t/MetaSeq......................ok
t/MicrosatelliteMarker.........ok
t/MiniMIMentry.................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/MitoProt.....................ok
t/Molphy.......................ok
t/multiple_fasta...............ok
t/Mutation.....................ok
t/Mutator......................ok
t/NetPhos...................... Failed 2/14 subtests
t/Node.........................ok
t/OddCodes.....................ok
t/OMIMentry....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/OMIMentryAllelicVariant......Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/OMIMparser...................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/Ontology.....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
set_attribute: not a compat02 graph at /home/src/perl/repoperls/installed-perls/maint-5.10/piB7lpk/perl-5.10.0@33412/lib/site_perl/5.10.0/Graph.pm line 2394, <GEN0> line 10.
Dubious, test returned 9 (wstat 2304, 0x900)
Failed 50/50 subtests
t/OntologyEngine...............Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/PAML.........................ok
t/Perl.........................Use of uninitialized value $au in substitution (s///) at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/SeqIO/swiss.pm line 855, <STREAM> line 43.
ok
t/phd..........................ok
t/Phenotype....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/PhylipDist...................ok
t/pICalculator.................ok
t/Pictogram....................ok
t/PopGen.......................ok
t/PopGenSims...................ok
t/primaryqual..................ok
t/PrimarySeq...................ok
t/primedseq....................ok
t/Primer.......................ok
t/primer3......................ok
t/Promoterwise.................ok
t/ProtDist.....................ok
t/psm..........................ok
t/QRNA.........................ok
t/qual.........................ok
t/RandDistFunctions............ok
t/RandomTreeFactory............ok
t/Range........................ok
t/RangeI.......................ok
t/RefSeq.......................ok
t/Registry.....................ok
t/Relationship.................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/RelationshipType.............Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/RemoteBlast..................ok
t/RepeatMasker.................ok
t/RestrictionAnalysis..........ok
t/RestrictionEnzyme............ok
t/RestrictionIO................ok
t/RNAChange....................ok
t/RootI........................ok
t/RootIO.......................ok
t/RootStorable.................ok
t/Scansite.....................ok
t/scf..........................ok
t/SearchDist...................ok
t/SearchIO.....................ok
t/Seq..........................ok
t/SeqAnalysisParser............ok
t/SeqBuilder...................ok
t/SeqDiff......................ok
t/SeqFeatCollection............ok
t/SeqFeature...................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/seqfeaturePrimer.............ok
t/SeqIO........................ok
t/SeqPattern...................ok
t/SeqStats.....................ok
t/SequenceFamily...............ok
t/sequencetrace................ok
t/SeqUtils.....................ok
t/seqwithquality...............ok
t/SeqWords.....................ok
t/Sigcleave....................ok
t/Sim4.........................ok
t/SimilarityPair...............ok
t/SimpleAlign..................ok
t/simpleGOparser...............Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
set_attribute: not a compat02 graph at /home/src/perl/repoperls/installed-perls/maint-5.10/piB7lpk/perl-5.10.0@33412/lib/site_perl/5.10.0/Graph.pm line 2394, <GEN1> line 14.
Dubious, test returned 9 (wstat 2304, 0x900)
Failed 98/98 subtests
t/sirna........................ok
t/SiteMatrix...................ok
t/SNP..........................ok
t/Sopma........................ok
t/Species......................ok
t/splicedseq...................ok
t/StandAloneBlast..............ok
t/StructIO.....................ok
t/Structure....................ok
t/Swiss........................ok
t/Symbol.......................ok
t/Taxonomy.....................ok
t/Tempfile.....................ok
t/Term.........................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/Bio/Root/Object.pm line 699.
ok
t/Tools........................ok
t/Tree.........................ok
t/TreeIO....................... All 41 subtests passed
t/trim.........................ok
t/tutorial.....................Use of uninitialized value $au in substitution (s///) at Bio/SeqIO/swiss.pm line 855, <STREAM> line 43.
Use of uninitialized value in print at /home/sand/.cpan/build/bioperl-1.4-9kBYZU/blib/lib/bptutorial.pl line 4042, <GEN21> line 934.
ok
t/UCSCParsers..................ok
t/Unflattener..................ok
t/Unflattener2.................ok
t/UniGene......................ok
t/Variation_IO.................1d0
<
32d30
<
60d57
<
91d87
<
121d116
<
152d146
<
183d176
<
214d206
<
245d236
<
268d258
<
291d280
<
315d303
<
347d334
<
379d365
<
1d0
<
1,350c1,388
< ID M20132:(362)c.+4G>A; E2K
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: 4
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 4 (M20132::366)
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature /codon_table: 1
< Feature /codon: gaa>aaa; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, conservative
< Feature /proof: computed
< Feature /location: 2
< Feature /change: E>K
< //
< ID M20132:(362)c.+14T>A; L5X
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: 14
< Feature /upflank: ccaagctcaaggatggaagtgcagt
< Feature /change: t>a
< Feature /dnflank: agggctgggaagggtctaccctcgg
< Feature RNA; 1
< Feature /label: nonsense
< Feature /proof: experimental
< Feature /location: 14 (M20132::376)
< Feature /upflank: ccaagctcaaggatggaagtgcagt
< Feature /change: t>a
< Feature /dnflank: agggctgggaagggtctaccctcgg
< Feature /codon_table: 1
< Feature /codon: tta>taa; 2
< Feature /region: coding
< Feature AA; 1
< Feature /label: truncation
< Feature /proof: computed
< Feature /location: 5
< Feature /change: L>*
< //
< ID M20132:(362)c.+4G>A; E2K
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: 4
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 4 (M20132::366)
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature /codon_table: 1
< Feature /codon: gaa>aaa; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, conservative
< Feature /proof: computed
< Feature /location: 2
< Feature /change: E>K
< //
< ID M20132:(362)c.+100delATCCAG; I34del-2
< Feature DNA; 1
< Feature /label: deletion
< Feature /proof: computed
< Feature /location: 100..105
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: atccag>
< Feature /dnflank: aacccgggccccaggcacccagagg
< Feature /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
< Feature RNA; 1
< Feature /label: inframe, deletion
< Feature /proof: experimental
< Feature /location: 100..105 (M20132::462..467)
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: atccag>
< Feature /dnflank: aacccgggccccaggcacccagagg
< Feature /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
< Feature /codon_table: 1
< Feature /codon: atc>-; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: deletion
< Feature /proof: computed
< Feature /location: 34..35
< Feature /change: IQ>
< //
< ID M20132:(362)c.+101delT; I34delX172
< Feature DNA; 1
< Feature /label: deletion
< Feature /proof: computed
< Feature /location: 101
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: t>
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
< Feature RNA; 1
< Feature /label: frameshift, deletion
< Feature /proof: experimental
< Feature /location: 101 (M20132::463)
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: t>
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
< Feature /codon_table: 1
< Feature /codon: atc>-; 2
< Feature /region: coding
< Feature AA; 1
< Feature /label: out-of-frame translation, truncation
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAP
< Feature GSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPAR
< Feature GCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*
< //
< ID M20132:(362)c.+101insGGGCCC; I34ins+2
< Feature DNA; 1
< Feature /label: insertion
< Feature /proof: computed
< Feature /location: 100^101
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: >gggccc
< Feature /dnflank: tccagaacccgggccccaggcaccc
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
< Feature +SduI
< Feature RNA; 1
< Feature /label: inframe, insertion
< Feature /proof: experimental
< Feature /location: 100^101 (M20132::462^463)
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: >gggccc
< Feature /dnflank: tccagaacccgggccccaggcaccc
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
< Feature +SduI
< Feature /codon_table: 1
< Feature /codon: atc>-; 2
< Feature /region: coding
< Feature AA; 1
< Feature /label: insertion, complex
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>RAL
< //
< ID M20132:(362)c.+100insG; I34ins81X
< Feature DNA; 1
< Feature /label: insertion
< Feature /proof: computed
< Feature /location: 99^100
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: >g
< Feature /dnflank: atccagaacccgggccccaggcacc
< Feature /re_site: +BamHI, +BinI, +NlaIV, +XhoII
< Feature RNA; 1
< Feature /label: frameshift, insertion
< Feature /proof: experimental
< Feature /location: 99^100 (M20132::461^462)
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: >g
< Feature /dnflank: atccagaacccgggccccaggcacc
< Feature /re_site: +BamHI, +BinI, +NlaIV, +XhoII
< Feature /codon_table: 1
< Feature /codon: atc>-; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: out-of-frame translation, truncation
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
< //
< ID M20132:(362)c.+100AT>GGGCCC; I34ins82X
< Feature DNA; 1
< Feature /label: complex
< Feature /proof: computed
< Feature /location: 100..101
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: at>gggccc
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
< Feature RNA; 1
< Feature /label: frameshift, complex
< Feature /proof: experimental
< Feature /location: 100..101 (M20132::462..463)
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: at>gggccc
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
< Feature /codon_table: 1
< Feature /codon: atc>-; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: out-of-frame translation, truncation
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
< //
< ID M20132:(362+1)c.-1G>A
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: -1
< Feature /upflank: ggtggaagattcagccaagctcaag
< Feature /change: g>a
< Feature /dnflank: atggaagtgcagttagggctgggaa
< Feature /re_site: -BccI, -FokI, +Hpy178III
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: experimental
< Feature /location: -1 (M20132::361)
< Feature /upflank: ggtggaagattcagccaagctcaag
< Feature /change: g>a
< Feature /dnflank: atggaagtgcagttagggctgggaa
< Feature /re_site: -BccI, -FokI, +Hpy178III
< Feature /region: 5'UTR
< //
< ID M20132:(362)c.+2766T>C
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: 2766
< Feature /upflank: tctatttccacacccagtgaagcat
< Feature /change: t>c
< Feature /dnflank: ggaaaccctatttccccaccccagc
< Feature /re_site: +Hpy188I, +SfaNI, -XcmI
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: experimental
< Feature /location: 2766 (M20132::3128)
< Feature /upflank: tctatttccacacccagtgaagcat
< Feature /change: t>c
< Feature /dnflank: ggaaaccctatttccccaccccagc
< Feature /re_site: +Hpy188I, +SfaNI, -XcmI
< Feature /region: 3'UTR
< //
< ID J02933:(521)g.+12165A>G
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: experimental
< Feature /location: 12165 (J02933::12686)
< Feature /upflank: cgcacacctgtggtgcctgccaccc
< Feature /change: a>g
< Feature /dnflank: ctgggttgcccatgattcatttttg
< Feature /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
< Feature -TspRI
< Feature /region: 3'UTR; (+1027)
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: computed
< Feature /location: 2428
< Feature /upflank: cgcacacctgtggtgcctgccaccc
< Feature /change: a>g
< Feature /dnflank: ctgggttgcccatgattcatttttg
< Feature /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
< Feature -TspRI
< Feature /region: 3'UTR; (-1)
< //
< ID J02933:(521)g.+4G>T; V2F
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: 4 (J02933::525)
< Feature /upflank: gcagcactgcagagatttcatcatg
< Feature /change: g>t
< Feature /dnflank: tctcccaggccctcaggctcctctg
< Feature /re_site: -BsmAI, -Eco31I
< Feature /region: exon; 1 (+4)
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 4
< Feature /upflank: gcagcactgcagagatttcatcatg
< Feature /change: g>t
< Feature /dnflank: tctcccaggccctcaggctcctctg
< Feature /re_site: -BsmAI, -Eco31I
< Feature /codon_table: 1
< Feature /codon: gtc>ttc; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, nonconservative
< Feature /proof: computed
< Feature /location: 2
< Feature /change: V>F
< //
< ID J02933:(521)g.+1168G>T; D34Y
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: 1168 (J02933::1689)
< Feature /upflank: taaggcctcaggaggagaaacacgg
< Feature /change: g>t
< Feature /dnflank: acatgccgtggaagccggggcctca
< Feature /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
< Feature +Tsp4CI
< Feature /region: exon; 1 (-29)
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 100
< Feature /upflank: taaggcctcaggaggagaaacacgg
< Feature /change: g>t
< Feature /dnflank: acatgccgtggaagccggggcctca
< Feature /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
< Feature +Tsp4CI
< Feature /codon_table: 1
< Feature /codon: gac>tac; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, nonconservative
< Feature /proof: computed
< Feature /location: 34
< Feature /change: D>Y
< //
< ID J02933:(521+1)g.-4C>G
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: -4 (J02933::518)
< Feature /upflank: ggcaggggcagcactgcagagattt
< Feature /change: c>g
< Feature /dnflank: atcatggtctcccaggccctcaggc
< Feature /re_site: +BclI, +DpnI, +MboI
< Feature /region: 5'UTR; (-4)
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: experimental
< Feature /location: -4
< Feature /upflank: ggcaggggcagcactgcagagattt
< Feature /change: c>g
< Feature /dnflank: atcatggtctcccaggccctcaggc
< Feature /re_site: +BclI, +DpnI, +MboI
< Feature /region: 5'UTR; (+31)
< //
---
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G>A" trivname="E2K">
> <DNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <restriction_changes>-BccI</restriction_changes>
> </DNA>
> <RNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <codon codon_ori="gaa" codon_mut="aaa" codon_pos="1"></codon>
> <restriction_changes>-BccI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="2" end="2" length="1" isMutation="1">
> <label>substitution</label>
> <label>conservative</label>
> <proof>computed</proof>
> <allele_ori>E</allele_ori>
> <allele_mut>K</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+14T>A" trivname="L5X">
> <DNA number="1" start="14" end="14" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>ccaagctcaaggatggaagtgcagt</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>agggctgggaagggtctaccctcgg</dnFlank>
> </DNA>
> <RNA number="1" start="14" end="14" length="1" isMutation="1">
> <label>nonsense</label>
> <proof>experimental</proof>
> <upFlank>ccaagctcaaggatggaagtgcagt</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>agggctgggaagggtctaccctcgg</dnFlank>
> <codon codon_ori="tta" codon_mut="taa" codon_pos="2"></codon>
> <region>coding</region>
> </RNA>
> <AA number="1" start="5" end="5" length="1" isMutation="1">
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>L</allele_ori>
> <allele_mut>*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G>A" trivname="E2K">
> <DNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <restriction_changes>-BccI</restriction_changes>
> </DNA>
> <RNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <codon codon_ori="gaa" codon_mut="aaa" codon_pos="1"></codon>
> <restriction_changes>-BccI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="2" end="2" length="1" isMutation="1">
> <label>substitution</label>
> <label>conservative</label>
> <proof>computed</proof>
> <allele_ori>E</allele_ori>
> <allele_mut>K</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100delATCCAG" trivname="I34del-2">
> <DNA number="1" start="100" end="105" length="6" isMutation="1">
> <label>deletion</label>
> <proof>computed</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>atccag</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>aacccgggccccaggcacccagagg</dnFlank>
> <restriction_changes>-BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV</restriction_changes>
> </DNA>
> <RNA number="1" start="100" end="105" length="6" isMutation="1">
> <label>inframe</label>
> <label>deletion</label>
> <proof>experimental</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>atccag</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>aacccgggccccaggcacccagagg</dnFlank>
> <codon codon_ori="atc" codon_pos="1"></codon>
> <restriction_changes>-BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="35" length="2" isMutation="1">
> <label>deletion</label>
> <proof>computed</proof>
> <allele_ori>IQ</allele_ori>
> <allele_mut></allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101delT" trivname="I34delX172">
> <DNA number="1" start="101" end="101" length="1" isMutation="1">
> <label>deletion</label>
> <proof>computed</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <restriction_changes>-BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I</restriction_changes>
> </DNA>
> <RNA number="1" start="101" end="101" length="1" isMutation="1">
> <label>frameshift</label>
> <label>deletion</label>
> <proof>experimental</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <codon codon_ori="atc" codon_pos="2"></codon>
> <restriction_changes>-BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>out-of-frame translation</label>
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAPGSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPARGCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101insGGGCCC" trivname="I34ins+2">
> <DNA number="1" start="101" end="101" length="0" isMutation="1">
> <label>insertion</label>
> <proof>computed</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>tccagaacccgggccccaggcaccc</dnFlank>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI</restriction_changes>
> </DNA>
> <RNA number="1" start="101" end="101" length="0" isMutation="1">
> <label>inframe</label>
> <label>insertion</label>
> <proof>experimental</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>tccagaacccgggccccaggcaccc</dnFlank>
> <codon codon_ori="atc" codon_pos="2"></codon>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>insertion</label>
> <label>complex</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>RAL</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100insG" trivname="I34ins81X">
> <DNA number="1" start="100" end="100" length="0" isMutation="1">
> <label>insertion</label>
> <proof>computed</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atccagaacccgggccccaggcacc</dnFlank>
> <restriction_changes>+BamHI, +BinI, +NlaIV, +XhoII</restriction_changes>
> </DNA>
> <RNA number="1" start="100" end="100" length="0" isMutation="1">
> <label>frameshift</label>
> <label>insertion</label>
> <proof>experimental</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atccagaacccgggccccaggcacc</dnFlank>
> <codon codon_ori="atc" codon_pos="1"></codon>
> <restriction_changes>+BamHI, +BinI, +NlaIV, +XhoII</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>out-of-frame translation</label>
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100AT>GGGCCC" trivname="I34ins82X">
> <DNA number="1" start="100" end="101" length="2" isMutation="1">
> <label>complex</label>
> <proof>computed</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>at</allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI</restriction_changes>
> </DNA>
> <RNA number="1" start="100" end="101" length="2" isMutation="1">
> <label>frameshift</label>
> <label>complex</label>
> <proof>experimental</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>at</allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <codon codon_ori="atc" codon_pos="1"></codon>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>out-of-frame translation</label>
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.-1G>A">
> <DNA number="1" start="-1" end="-1" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>ggtggaagattcagccaagctcaag</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>atggaagtgcagttagggctgggaa</dnFlank>
> <restriction_changes>-BccI, -FokI, +Hpy178III</restriction_changes>
> </DNA>
> <RNA number="1" start="-1" end="-1" length="1" isMutation="1">
> <label>unknown</label>
> <proof>experimental</proof>
> <upFlank>ggtggaagattcagccaagctcaag</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>atggaagtgcagttagggctgggaa</dnFlank>
> <restriction_changes>-BccI, -FokI, +Hpy178III</restriction_changes>
> <region>5'UTR</region>
> </RNA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+2766T>C">
> <DNA number="1" start="2766" end="2766" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>tctatttccacacccagtgaagcat</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>c</allele_mut>
> <dnFlank>ggaaaccctatttccccaccccagc</dnFlank>
> <restriction_changes>+Hpy188I, +SfaNI, -XcmI</restriction_changes>
> </DNA>
> <RNA number="1" start="2766" end="2766" length="1" isMutation="1">
> <label>unknown</label>
> <proof>experimental</proof>
> <upFlank>tctatttccacacccagtgaagcat</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>c</allele_mut>
> <dnFlank>ggaaaccctatttccccaccccagc</dnFlank>
> <restriction_changes>+Hpy188I, +SfaNI, -XcmI</restriction_changes>
> <region>3'UTR</region>
> </RNA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+12165A>G">
> <DNA number="1" start="12165" end="12165" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>experimental</proof>
> <upFlank>cgcacacctgtggtgcctgccaccc</upFlank>
> <allele_ori>a</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>ctgggttgcccatgattcatttttg</dnFlank>
> <restriction_changes>+AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI</restriction_changes>
> <region dist="1027">3'UTR</region>
> </DNA>
> <RNA number="1" start="2428" end="2428" length="1" isMutation="1">
> <label>unknown</label>
> <proof>computed</proof>
> <upFlank>cgcacacctgtggtgcctgccaccc</upFlank>
> <allele_ori>a</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>ctgggttgcccatgattcatttttg</dnFlank>
> <restriction_changes>+AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI</restriction_changes>
> <region dist="-1">3'UTR</region>
> </RNA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+4G>T" trivname="V2F">
> <DNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>gcagcactgcagagatttcatcatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>tctcccaggccctcaggctcctctg</dnFlank>
> <restriction_changes>-BsmAI, -Eco31I</restriction_changes>
> <region value="1" dist="4">exon</region>
> </DNA>
> <RNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>gcagcactgcagagatttcatcatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>tctcccaggccctcaggctcctctg</dnFlank>
> <codon codon_ori="gtc" codon_mut="ttc" codon_pos="1"></codon>
> <restriction_changes>-BsmAI, -Eco31I</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="2" end="2" length="1" isMutation="1">
> <label>substitution</label>
> <label>nonconservative</label>
> <proof>computed</proof>
> <allele_ori>V</allele_ori>
> <allele_mut>F</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+1168G>T" trivname="D34Y">
> <DNA number="1" start="1168" end="1168" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>taaggcctcaggaggagaaacacgg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>acatgccgtggaagccggggcctca</dnFlank>
> <restriction_changes>-BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI</restriction_changes>
> <region value="1" dist="-29">exon</region>
> </DNA>
> <RNA number="1" start="100" end="100" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>taaggcctcaggaggagaaacacgg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>acatgccgtggaagccggggcctca</dnFlank>
> <codon codon_ori="gac" codon_mut="tac" codon_pos="1"></codon>
> <restriction_changes>-BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>substitution</label>
> <label>nonconservative</label>
> <proof>computed</proof>
> <allele_ori>D</allele_ori>
> <allele_mut>Y</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.-4C>G">
> <DNA number="1" start="-4" end="-4" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>ggcaggggcagcactgcagagattt</upFlank>
> <allele_ori>c</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atcatggtctcccaggccctcaggc</dnFlank>
> <restriction_changes>+BclI, +DpnI, +MboI</restriction_changes>
> <region dist="-4">5'UTR</region>
> </DNA>
> <RNA number="1" start="-4" end="-4" length="1" isMutation="1">
> <label>unknown</label>
> <proof>experimental</proof>
> <upFlank>ggcaggggcagcactgcagagattt</upFlank>
> <allele_ori>c</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atcatggtctcccaggccctcaggc</dnFlank>
> <restriction_changes>+BclI, +DpnI, +MboI</restriction_changes>
> <region dist="31">5'UTR</region>
> </RNA>
> </seqDiff>
Failed 3/25 subtests
t/WABA.........................ok
t/XEMBL_DB.....................ok
Test Summary Report
-------------------
t/BioFetch_DB.t (Wstat: 0 Tests: 27 Failed: 3)
Failed tests: 8, 20-21
t/DB.t (Wstat: 0 Tests: 78 Failed: 2)
Failed tests: 30-31
t/EMBL_DB.t (Wstat: 0 Tests: 15 Failed: 3)
Failed tests: 6, 13-14
t/MeSH.t (Wstat: 0 Tests: 26 Failed: 1)
Failed test: 26
t/NetPhos.t (Wstat: 0 Tests: 14 Failed: 2)
Failed tests: 10, 13
t/Ontology.t (Wstat: 2304 Tests: 0 Failed: 0)
Non-zero exit status: 9
Parse errors: Bad plan. You planned 50 tests but ran 0.
t/simpleGOparser.t (Wstat: 2304 Tests: 0 Failed: 0)
Non-zero exit status: 9
Parse errors: Bad plan. You planned 98 tests but ran 0.
t/TreeIO.t (Wstat: 0 Tests: 42 Failed: 1)
Failed test: 42
Parse errors: Bad plan. You planned 41 tests but ran 42.
t/Variation_IO.t (Wstat: 0 Tests: 25 Failed: 3)
Failed tests: 15, 20, 25
Files=179, Tests=8126, 221 wallclock secs ( 3.34 usr 0.40 sys + 124.69 cusr 7.03 csys = 135.46 CPU)
Result: FAIL
Failed 9/179 test programs. 15/8126 subtests failed.
make: *** [test_dynamic] Fehler 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
-------------- ---- ------
DB_File 0 1.817
File::Spec 0 3.2701
File::Temp 0 0.20
HTML::Entities 0 1.35
IO::Scalar 0 2.110
IO::String 0 1.08
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = de_DE.UTF-8
PATH = /usr/lib/ccache:/home/sand/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/usr/local/perl/bin:/usr/X11/bin:/sbin:/usr/sbin
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 9506
PERL5_CPAN_IS_RUNNING = 9506
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/src/perl/repoperls/installed-perls/maint-5.10/piB7lpk/perl-5.10.0@33412/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- ---------
CPAN 1.92_60
Cwd 3.2701
ExtUtils::CBuilder 0.22
ExtUtils::Command 1.14
ExtUtils::Install 1.50
ExtUtils::MakeMaker 6.44
ExtUtils::Manifest 1.51_01
ExtUtils::ParseXS 2.18_02
File::Spec 3.2701
Module::Build 0.2808_01
Module::Signature 0.55
Test::Harness 3.10
Test::More 0.80
YAML 0.66
YAML::Syck 1.04
version 0.74
--
Summary of my perl5 (revision 5 version 10 subversion 0 patch 33412) configuration:
Platform:
osname=linux, osvers=2.6.22-1-k7, archname=i686-linux-thread-multi-64int
uname='linux k75 2.6.22-1-k7 #1 smp sun jul 29 15:15:55 utc 2007 i686 gnulinux '
config_args='-Dprefix=/home/src/perl/repoperls/installed-perls/maint-5.10/piB7lpk/perl-5.10.0@33412 -Dinstallusrbinperl=n -Uversiononly -Dusedevel -des -Ui_db -Dusethreads -Duse64bitint'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -I/usr/local/include'
ccversion='', gccversion='4.1.2 20061115 (prerelease) (Debian 4.1.1-21)', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -L/usr/local/lib'
libpth=/usr/local/lib /lib /usr/lib /usr/lib64
libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=/lib/libc-2.7.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.7'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib'
-
FAIL bioperl-1.4 i686-linux-thread-multi-64int 2.6.22-1-k7
by andreas.koenig.gmwojprw