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FAIL bioperl-1.4 i686-linux-64int 2.6.22-1-k7
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From:
andreas.koenig.gmwojprw
Date:
September 10, 2007 07:39
Subject:
FAIL bioperl-1.4 i686-linux-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/
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 test report for bioperl-1.4, created
automatically by CPAN::Reporter, version 0.99_07, and sent to the CPAN
Testers mailing list. If you have received this email directly, it is
because the person testing your distribution chose to send a copy to your
CPAN email address; there may be a delay before the official report is
received and processed by CPAN Testers.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
Sections of this report:
* Tester comments
* Prerequisites
* Environment and other context
* Test output
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
[none provided]
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
-------------- ---- -----
DB_File 0 1.815
File::Spec 0 3.25
File::Temp 0 0.18
HTML::Entities 0 1.35
IO::Scalar 0 2.110
IO::String 0 1.08
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
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 =
PERL5_CPANPLUS_IS_RUNNING = 31042
PERL5_CPAN_IS_RUNNING = 31042
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /home/src/perl/repoperls/installed-perls/perl/pNUSF0c/perl-5.8.0@31684/bin/perl
UID: $< = 1005
EUID: $> = 1005
GID: $( = 1005 1005
EGID: $) = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- -------
CPAN 1.9102
Cwd 3.25
ExtUtils::CBuilder 0.19
ExtUtils::Command 1.13
ExtUtils::Install 1.44
ExtUtils::MakeMaker 6.36
ExtUtils::Manifest 1.51_01
ExtUtils::ParseXS 2.18
File::Spec 3.25
Module::Build 0.2808
Module::Signature 0.55
Test::Harness 2.99_02
Test::More 0.70
YAML 0.65
YAML::Syck 0.97
version 0.7203
------------------------------
TEST OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 /home/src/perl/repoperls/installed-perls/perl/pNUSF0c/perl-5.8.0@31684/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-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
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 1/27 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-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
ok
t/CytoMap......................ok
t/DB...........................ok
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-BihuUR/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: Mon, 10 Sep 2007 14:31:04 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-BihuUR/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-BihuUR/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /home/sand/.cpan/build/bioperl-1.4-BihuUR/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-BihuUR/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-BihuUR/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-BihuUR/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-BihuUR/blib/lib/Bio/DB/MeSH.pm line 263.
Use of uninitialized value $name in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-BihuUR/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value $name in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-BihuUR/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value $name in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-BihuUR/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-BihuUR/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......................ok
t/Node.........................ok
t/OddCodes.....................ok
t/OMIMentry....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
ok
t/OMIMentryAllelicVariant......Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
ok
t/OMIMparser...................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
ok
t/Ontology.....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
set_attribute: not a compat02 graph at /home/src/perl/repoperls/installed-perls/perl/pNUSF0c/perl-5.8.0@31684/lib/site_perl/5.9.5/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-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
ok
t/PAML.........................ok
t/Perl.........................ok
t/phd..........................ok
t/Phenotype....................Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-BihuUR/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-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
ok
t/RelationshipType.............Useless localization of scalar assignment at /home/sand/.cpan/build/bioperl-1.4-BihuUR/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-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
-------------------- WARNING ---------------------
MSG: acc (gb|AY095304) does not exist
---------------------------------------------------
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-BihuUR/blib/lib/Bio/Root/Object.pm line 699.
set_attribute: not a compat02 graph at /home/src/perl/repoperls/installed-perls/perl/pNUSF0c/perl-5.8.0@31684/lib/site_perl/5.9.5/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-BihuUR/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 in print at /home/sand/.cpan/build/bioperl-1.4-BihuUR/blib/lib/bptutorial.pl line 4042, <GEN20> 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/Biblio.t (Wstat: 0 Tests: 24 Failed: 0)
Tests skipped: 2
t/BioFetch_DB.t (Wstat: 0 Tests: 27 Failed: 1)
Failed tests: 8
t/EMBL_DB.t (Wstat: 0 Tests: 15 Failed: 3)
Failed tests: 6, 13-14
t/Genewise.t (Wstat: 0 Tests: 51 Failed: 0)
Tests skipped: 33-34
t/MeSH.t (Wstat: 0 Tests: 26 Failed: 1)
Failed tests: 26
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/RemoteBlast.t (Wstat: 0 Tests: 6 Failed: 0)
Tests skipped: 3-6
t/SeqIO.t (Wstat: 0 Tests: 235 Failed: 0)
Tests skipped: 68, 114, 126
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/Taxonomy.t (Wstat: 0 Tests: 8 Failed: 0)
Tests skipped: 2-8
t/TreeIO.t (Wstat: 0 Tests: 42 Failed: 1)
Failed tests: 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, 539 wallclock secs (234.55 cusr + 7.51 csys = 242.06 CPU)
Result: FAIL
Failed 7/179 test programs. 9/8126 subtests failed.
make: *** [test_dynamic] Error 255
--
Summary of my perl5 (revision 5 version 9 subversion 5) configuration:
Platform:
osname=linux, osvers=2.6.22-1-k7, archname=i686-linux-64int
uname='linux k75 2.6.22-1-k7 #1 smp mon jul 23 14:02:09 utc 2007 i686 gnulinux '
config_args='-Dprefix=/home/src/perl/repoperls/installed-perls/perl/pNUSF0c/perl-5.8.0@31684 -Dinstallusrbinperl=n -Uversiononly -Doptimize=-g -des -Duse64bitint -Dusedevel'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-g',
cppflags='-DDEBUGGING -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 -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
libc=/lib/libc-2.6.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.6'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -g -L/usr/local/lib'
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