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FAIL bioperl-1.4 i386-linux-thread-multi 2.6.18-53.el5
From:
ICERIDER
Date:
May 15, 2008 19:41
Subject:
FAIL bioperl-1.4 i386-linux-thread-multi 2.6.18-53.el5
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 cpan-testers@perl.org to keep other
test volunteers informed and to prevent any duplicate effort.
--
Dear Ewan Birney,
This is a computer-generated report for bioperl-1.4
on perl 5.8.8, created by CPAN-Reporter-1.13.
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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 /usr/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...................ok
t/AnnotationAdaptor............ok
t/Assembly.....................ok
t/Biblio.......................SOAP::Lite not installed. Skipping some tests.
ok
t/Biblio_biofetch..............ok
t/BiblioReferences.............ok
t/BioDBGFF.....................ok
t/BioFetch_DB.................. Failed 3/27 subtests
t/BioGraphics..................GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.
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....................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.....................ok
t/ELM..........................
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 URL must be absolute
Content-Type: text/plain
Client-Date: Fri, 16 May 2008 02:35:52 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/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/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/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /home/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/blib/lib/Bio/Root/IO.pm line 440.
ok
t/GOR4.........................ok
t/GOterm.......................ok
t/GuessSeqFormat...............ok
t/hmmer........................ok
t/HNN..........................ok
t/Index........................ok
t/InstanceSite.................ok
t/InterProParser...............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....................ok
t/lucy.........................ok
t/Map..........................ok
t/MapIO........................ok
t/Matrix.......................ok
t/Measure......................ok
t/MeSH.........................Use of uninitialized value in substitution (s///) at /home/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/blib/lib/Bio/DB/MeSH.pm line 263.
Use of uninitialized value in regexp compilation at /home/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value in regexp compilation at /home/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value in regexp compilation at /home/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/blib/lib/Bio/DB/MeSH.pm line 277.
Failed 1/26 subtests
t/MetaSeq......................ok
t/MicrosatelliteMarker.........ok
t/MiniMIMentry.................ok
t/MitoProt.....................ok
t/Molphy.......................ok
t/multiple_fasta...............ok
t/Mutation.....................ok
t/Mutator......................ok
t/NetPhos......................ok
t/Node.........................ok
t/OddCodes.....................ok
t/OMIMentry....................ok
t/OMIMentryAllelicVariant......ok
t/OMIMparser...................ok
t/Ontology.....................
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...
ok
t/OntologyEngine...............ok
t/PAML.........................ok
t/Perl.........................Use of uninitialized value in substitution (s///) at /home/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/blib/lib/Bio/SeqIO/swiss.pm line 855, <STREAM> line 43.
ok
t/phd..........................ok
t/Phenotype....................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.................ok
t/RelationshipType.............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...................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...............
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...
ok
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.........................ok
t/Tools........................ok
t/Tree.........................ok
t/TreeIO.......................ok
t/trim.........................ok
t/tutorial.....................Use of uninitialized value in substitution (s///) at Bio/SeqIO/swiss.pm line 855, <STREAM> line 43.
Use of uninitialized value in print at /home/icerider70/.cpan/build/bioperl-1.4-B5ZDd0/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.....................SOAP::Lite and/or XML::DOM not installed. This means that Bio::DB::XEMBL module is not usable. Skipping tests.
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/Variation_IO.t (Wstat: 0 Tests: 25 Failed: 3)
Failed tests: 15, 20, 25
Files=179, Tests=8127, 423 wallclock secs ( 8.64 usr 1.33 sys + 289.69 cusr 30.50 csys = 330.16 CPU)
Result: FAIL
Failed 5/179 test programs. 12/8127 subtests failed.
make: *** [test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
-------------- ---- -----
DB_File 0 1.814
File::Spec 0 3.27
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:
DBIC_NO_WARN_BAD_PERL = 1
LANG = en_US.UTF-8
PATH = /usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/icerider70/bin
PERL5LIB = /home/icerider70/.cpan/build/Class-MethodMaker-2.11-3q85en/blib/arch:/home/icerider70/.cpan/build/Class-MethodMaker-2.11-3q85en/blib/lib:/home/icerider70/.cpan/build/Lingua-Translit-0.10-LxiPDE/blib/arch:/home/icerider70/.cpan/build/Lingua-Translit-0.10-LxiPDE/blib/lib:/home/icerider70/.cpan/build/PerlIO-Util-0.03-3VxGCc/blib/arch:/home/icerider70/.cpan/build/PerlIO-Util-0.03-3VxGCc/blib/lib:/home/icerider70/.cpan/build/POE-Component-Client-opentick-0.15-YnJ7ec/blib/arch:/home/icerider70/.cpan/build/POE-Component-Client-opentick-0.15-YnJ7ec/blib/lib:/home/icerider70/.cpan/build/Filter-SQL-0.05-jVsty8/blib/arch:/home/icerider70/.cpan/build/Filter-SQL-0.05-jVsty8/blib/lib:/home/icerider70/.cpan/build/Linux-DVB-1.0-tE3j1a/blib/arch:/home/icerider70/.cpan/build/Linux-DVB-1.0-tE3j1a/blib/lib:/home/icerider70/.cpan/build/Chooser-1.1.5-Llys6z/blib/arch:/home/icerider70/.cpan/build/Chooser-1.1.5-Llys6z/blib/lib:/home/icerider70/.cpan/build/Audio-FindChunks-1.00-QOIbFs/
blib/arch:/home/icerider70/.cpan/build/Audio-FindChunks-1.00-QOIbFs/blib/lib:/home/icerider70/.cpan/build/Data-Flow-1.02-ooJz4u/blib/arch:/home/icerider70/.cpan/build/Data-Flow-1.02-ooJz4u/blib/lib:/home/icerider70/.cpan/build/Text-Template-1.45-r7xHdO/blib/arch:/home/icerider70/.cpan/build/Text-Template-1.45-r7xHdO/blib/lib:/home/icerider70/.cpan/build/WWW-MySociety-Gaze-0.02-WWsHWx/blib/arch:/home/icerider70/.cpan/build/WWW-MySociety-Gaze-0.02-WWsHWx/blib/lib:/home/icerider70/.cpan/build/HTML-Tiny-1.01-FD6rF1/blib/arch:/home/icerider70/.cpan/build/HTML-Tiny-1.01-FD6rF1/blib/lib:/home/icerider70/.cpan/build/Text-CSV-1.05-cH3xJS/blib/arch:/home/icerider70/.cpan/build/Text-CSV-1.05-cH3xJS/blib/lib:/home/icerider70/.cpan/build/Net-MRIM-1.08-W_NUAC/blib/arch:/home/icerider70/.cpan/build/Net-MRIM-1.08-W_NUAC/blib/lib:/home/icerider70/.cpan/build/SQL-Tokenizer-0.15-b5SM11/blib/arch:/home/icerider70/.cpan/build/SQL-Tokenizer-0.15-b5SM11/blib/lib
PERL5_CPANPLUS_IS_RUNNING = 9829
PERL5_CPAN_IS_RUNNING = 9829
PERL_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
PERL_TEST_CRITIC = 1
SHELL = /bin/bash
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/bin/perl
$UID/$EUID = 500 / 500
$GID = 500 500 37
$EGID = 500 500 37
Perl module toolchain versions installed:
Module Have
------------------- ------
CPAN 1.9205
Cwd 3.27
ExtUtils::CBuilder 0.21
ExtUtils::Command 1.13
ExtUtils::Install 1.45
ExtUtils::MakeMaker 6.44
ExtUtils::Manifest 1.51
ExtUtils::ParseXS 2.18
File::Spec 3.27
Module::Build 0.2808
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 8 subversion 8) configuration:
Platform:
osname=linux, osvers=2.6.18-53.el5, archname=i386-linux-thread-multi
uname='linux builder7.centos.org 2.6.9-42.0.3.elsmp #1 smp fri oct 6 06:21:39 cdt 2006 i686 i686 i386 gnulinux '
config_args='-des -Doptimize=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -Dversion=5.8.8 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dinstallprefix=/usr -Dprefix=/usr -Darchname=i386-linux -Dvendorprefix=/usr -Dsiteprefix=/usr -Duseshrplib -Dusethreads -Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dinc_version_list=5.8.7 5.8.6 5.8.5 -Dscriptdir=/usr/bin'
hint=recommended, useposix=true, d_sigaction=define
usethreads=define use5005threads=undef useithreads=define usemultiplicity=define
useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=undef use64bitall=undef uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm',
optimize='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -I/usr/include/gdbm'
ccversion='', gccversion='4.1.1 20061011 (Red Hat 4.1.1-30)', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define
Linker and Libraries:
ld='gcc', ldflags =' -L/usr/local/lib'
libpth=/usr/local/lib /lib /usr/lib
libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=/lib/libc-2.5.so, so=so, useshrplib=true, libperl=libperl.so
gnulibc_version='2.5'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E -Wl,-rpath,/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE'
cccdlflags='-fPIC', lddlflags='-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib'
-
FAIL bioperl-1.4 i386-linux-thread-multi 2.6.18-53.el5
by ICERIDER