[Bioperl-l] FW: load_seqdatabase.pl error
Forrest Zhang
forrest_zhang at 163.com
Fri Sep 28 05:34:21 UTC 2007
Oh, my God! I am tring reinstall bioperl-live using CVS, so many error
shown below.
biocc bioperl-live # perl Build.PL
Checking whether your kit is complete...
Looks good
Checking prerequisites...
Looks good
Checking features:
BioDBGFF.................enabled
BioDBSeqFeature_mysql....enabled
Network..................enabled
BioDBSeqFeature_BDB......enabled
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a]
- will install all scripts
Do you want to run the BioDBGFF live database tests? y/n [n] y
Which database should I use for testing the mysql driver? [test]
On which host is database 'test' running (hostname, ip address or host:port)
[localhost]
User name for connecting to database 'test'? [undef] root
Password for connecting to database 'test'? [undef]
- will run the BioDBGFF tests with database driver 'mysql' and these
settings:
Database test
Host localhost
DSN dbi:mysql:database=test
User root
Password undef
Do you want to run tests that require connection to servers across the
internet
(likely to cause some failures)? y/n [n] y
- will run internet-requiring tests
Deleting Build
Removed previous script 'Build'
Creating new 'Build' script for 'bioperl' version '1.0050021'
biocc bioperl-live # ./Build test
Copying Bio/Align/Utilities.pm -> blib/lib/Bio/Align/Utilities.pm
Copying Bio/Search/HSP/ModelHSP.pm -> blib/lib/Bio/Search/HSP/ModelHSP.pm
Copying Bio/Ontology/DocumentRegistry.pm ->
blib/lib/Bio/Ontology/DocumentRegistry.pm
Copying Bio/SeqFeature/Annotated.pm -> blib/lib/Bio/SeqFeature/Annotated.pm
Copying Bio/SimpleAlign.pm -> blib/lib/Bio/SimpleAlign.pm
Copying Bio/AlignIO/stockholm.pm -> blib/lib/Bio/AlignIO/stockholm.pm
Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
Deleting blib/script/bp_sreformat.PLS.bak
blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
Copying scripts/graphics/contig_draw.PLS -> blib/script/contig_draw.PLS
Deleting blib/script/contig_draw.PLS.bak
blib/script/contig_draw.PLS -> blib/script/bp_contig_draw.pl
Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
Deleting blib/script/meta_gff.PLS.bak
blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
Deleting blib/script/tree2pag.PLS.bak
blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS ->
blib/script/bp_seqfeature_gff3.PLS
blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
Copying scripts/popgen/heterogeneity_test.PLS ->
blib/script/heterogeneity_test.PLS
Deleting blib/script/heterogeneity_test.PLS.bak
blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
Deleting blib/script/flanks.PLS.bak
blib/script/flanks.PLS -> blib/script/bp_flanks.pl
Copying scripts/graphics/feature_draw.PLS -> blib/script/feature_draw.PLS
Deleting blib/script/feature_draw.PLS.bak
blib/script/feature_draw.PLS -> blib/script/bp_feature_draw.pl
Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
Deleting blib/script/biogetseq.PLS.bak
blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS ->
blib/script/bp_seqfeature_load.PLS
Deleting blib/script/bp_seqfeature_load.PLS.bak
blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
Copying scripts/searchio/fastam9_to_table.PLS ->
blib/script/fastam9_to_table.PLS
Deleting blib/script/fastam9_to_table.PLS.bak
blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
Deleting blib/script/seq_length.PLS.bak
blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
Deleting blib/script/genbank2gff.PLS.bak
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
Deleting blib/script/taxid4species.PLS.bak
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
Copying scripts/biographics/bp_glyphs1-demo.PLS ->
blib/script/bp_glyphs1-demo.PLS
Deleting blib/script/bp_glyphs1-demo.PLS.bak
blib/script/bp_glyphs1-demo.PLS -> blib/script/bp_glyphs1-demo.pl
Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
Deleting blib/script/blast2tree.PLS.bak
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
Copying scripts/graphics/frend.PLS -> blib/script/frend.PLS
Deleting blib/script/frend.PLS.bak
blib/script/frend.PLS -> blib/script/bp_frend.pl
Copying scripts/taxa/query_entrez_taxa.PLS ->
blib/script/query_entrez_taxa.PLS
Deleting blib/script/query_entrez_taxa.PLS.bak
blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
Copying scripts/biographics/bp_glyphs2-demo.PLS ->
blib/script/bp_glyphs2-demo.PLS
Deleting blib/script/bp_glyphs2-demo.PLS.bak
blib/script/bp_glyphs2-demo.PLS -> blib/script/bp_glyphs2-demo.pl
Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
Deleting blib/script/taxonomy2tree.PLS.bak
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
Copying scripts/utilities/search2alnblocks.PLS ->
blib/script/search2alnblocks.PLS
Deleting blib/script/search2alnblocks.PLS.bak
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
Copying scripts/utilities/mask_by_search.PLS ->
blib/script/mask_by_search.PLS
Deleting blib/script/mask_by_search.PLS.bak
blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
Deleting blib/script/gccalc.PLS.bak
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
Deleting blib/script/composite_LD.PLS.bak
blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
Deleting blib/script/aacomp.PLS.bak
blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
Copying scripts/Bio-DB-GFF/process_wormbase.PLS ->
blib/script/process_wormbase.PLS
Deleting blib/script/process_wormbase.PLS.bak
blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
Copying scripts/taxa/local_taxonomydb_query.PLS ->
blib/script/local_taxonomydb_query.PLS
Deleting blib/script/local_taxonomydb_query.PLS.bak
blib/script/local_taxonomydb_query.PLS ->
blib/script/bp_local_taxonomydb_query.pl
Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
Deleting blib/script/biblio.PLS.bak
blib/script/biblio.PLS -> blib/script/bp_biblio.pl
Copying scripts/biographics/bp_embl2picture.PLS ->
blib/script/bp_embl2picture.PLS
Deleting blib/script/bp_embl2picture.PLS.bak
blib/script/bp_embl2picture.PLS -> blib/script/bp_embl2picture.pl
Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
Deleting blib/script/genbank2gff3.PLS.bak
blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
Deleting blib/script/search2BSML.PLS.bak
blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
Deleting blib/script/seqconvert.PLS.bak
blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
Copying scripts/searchio/parse_hmmsearch.PLS ->
blib/script/parse_hmmsearch.PLS
Deleting blib/script/parse_hmmsearch.PLS.bak
blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
Deleting blib/script/bp_seqret.PLS.bak
blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
Deleting blib/script/filter_search.PLS.bak
blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
Deleting blib/script/nexus2nh.PLS.bak
blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
Copying scripts/Bio-DB-GFF/generate_histogram.PLS ->
blib/script/generate_histogram.PLS
Deleting blib/script/generate_histogram.PLS.bak
blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
Deleting blib/script/split_seq.PLS.bak
blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
Deleting blib/script/load_gff.PLS.bak
blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
Deleting blib/script/bp_fetch.PLS.bak
blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
Deleting blib/script/mutate.PLS.bak
blib/script/mutate.PLS -> blib/script/bp_mutate.pl
Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
Deleting blib/script/process_sgd.PLS.bak
blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
Deleting blib/script/bp_index.PLS.bak
blib/script/bp_index.PLS -> blib/script/bp_index.pl
Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
Deleting blib/script/dbsplit.PLS.bak
blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
Deleting blib/script/oligo_count.PLS.bak
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
Copying scripts/searchio/hmmer_to_table.PLS ->
blib/script/hmmer_to_table.PLS
Deleting blib/script/hmmer_to_table.PLS.bak
blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
Copying scripts/Bio-DB-GFF/process_gadfly.PLS ->
blib/script/process_gadfly.PLS
Deleting blib/script/process_gadfly.PLS.bak
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
Copying scripts/DB/biofetch_genbank_proxy.PLS ->
blib/script/biofetch_genbank_proxy.PLS
Deleting blib/script/biofetch_genbank_proxy.PLS.bak
blib/script/biofetch_genbank_proxy.PLS ->
blib/script/bp_biofetch_genbank_proxy.pl
Copying scripts/seq/extract_feature_seq.PLS ->
blib/script/extract_feature_seq.PLS
Deleting blib/script/extract_feature_seq.PLS.bak
blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS ->
blib/script/bulk_load_gff.PLS
Deleting blib/script/bulk_load_gff.PLS.bak
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
Deleting blib/script/search2gff.PLS.bak
blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
Copying scripts/seq/make_mrna_protein.PLS ->
blib/script/make_mrna_protein.PLS
Deleting blib/script/make_mrna_protein.PLS.bak
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
Deleting blib/script/unflatten_seq.PLS.bak
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
Deleting blib/script/search2tribe.PLS.bak
blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
Deleting blib/script/bioflat_index.PLS.bak
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
Deleting blib/script/pairwise_kaks.PLS.bak
blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
Copying scripts/Bio-DB-GFF/fast_load_gff.PLS ->
blib/script/fast_load_gff.PLS
Deleting blib/script/fast_load_gff.PLS.bak
blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
Deleting blib/script/chaos_plot.PLS.bak
blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
Deleting blib/script/bp_mrtrans.PLS.bak
blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
Deleting blib/script/bp_nrdb.PLS.bak
blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
Copying scripts/taxa/classify_hits_kingdom.PLS ->
blib/script/classify_hits_kingdom.PLS
Deleting blib/script/classify_hits_kingdom.PLS.bak
blib/script/classify_hits_kingdom.PLS ->
blib/script/bp_classify_hits_kingdom.pl
Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
Deleting blib/script/remote_blast.PLS.bak
blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
Deleting blib/script/search2table.PLS.bak
blib/script/search2table.PLS -> blib/script/bp_search2table.pl
Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
Deleting blib/script/translate_seq.PLS.bak
blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
Copying scripts/graphics/search_overview.PLS ->
blib/script/search_overview.PLS
Deleting blib/script/search_overview.PLS.bak
blib/script/search_overview.PLS -> blib/script/bp_search_overview.pl
t/AAChange...................ok
t/AAReverseMutate............ok
t/AlignIO....................ok
t/AlignStats.................ok
t/AlignUtil..................ok
t/Allele.....................ok
t/Alphabet...................ok
t/Annotation.................ok 1/112
# Failed (TODO) test 'The object isa Bio::Annotation::Comment'
# at t/Annotation.t line 214.
# The object isn't a 'Bio::Annotation::Comment' it's a
'Bio::Annotation::OntologyTerm'
t/Annotation.................ok
1/112 unexpectedly succeeded
TODO PASSED test 96
t/AnnotationAdaptor..........ok
t/Assembly...................ok 1/35
# Failed (TODO) test 'get_nof_singlets'
# at t/Assembly.t line 44.
# got: '0'
# expected: '1'
# Failed (TODO) test 'get_seq_ids'
# at t/Assembly.t line 48.
# got: '0'
# expected: '2'
# Failed (TODO) test at t/Assembly.t line 53.
# '0'
# ne
# '0'
# Failed test at t/Assembly.t line 145.
# got: '_main_contig_feature:106'
# expected: '_aligned_coord:sdsu|SDSU_RFPERU_006_E04.x01.phd.1'
t/Assembly...................NOK 31/35# Looks like you failed 1 test of 35.
t/Assembly...................dubious
Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 31
Failed 1/35 tests, 97.14% okay
t/Biblio.....................ok
t/BiblioReferences...........ok
t/Biblio_biofetch............ok
t/Biblio_eutils..............ok
t/BioDBGFF...................ok
3/277 skipped: various reasons
t/BioDBSeqFeature............ok
t/BioDBSeqFeature_BDB........ok
t/BioDBSeqFeature_mysql......ok
t/BioFetch_DB................ok
t/BioGraphics................ok
t/BlastIndex.................ok
t/Chain......................ok
t/ClusterIO..................ok
t/Coalescent.................ok
t/CodonTable.................ok
t/Compatible.................ok
t/CoordinateGraph............ok
t/CoordinateMapper...........ok
t/Correlate..................ok
t/CytoMap....................ok
t/DB.........................ok 104/116Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 491.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 565.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 565.
t/DB.........................ok 107/116Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 565.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 372.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/Bio/SeqIO/entrezgene.pm line 565.
t/DB.........................ok
t/DBCUTG.....................ok
t/DBFasta....................ok
t/DNAMutation................ok
t/Domcut.....................ok
t/ECnumber...................ok
t/ELM........................ok
t/EMBL_DB....................ok
t/EMBOSS_Tools...............ok
t/ESEfinder..................ok
t/EUtilities.................skipped
all skipped: Must set BIOPERLDEBUG=1 for network tests
t/EncodedSeq.................ok
t/Exception..................ok
t/Exonerate..................ok
4/45 skipped: various reasons
t/FeatureIO..................ok
t/FootPrinter................ok
t/GDB........................ok
t/GFF........................ok
t/GOR4.......................ok
t/GOterm.....................ok
t/GbrowseGFF.................ok
t/Gel........................ok
t/GeneCoordinateMapper.......ok
t/Geneid.....................ok
t/Genewise...................ok 1/53
# Failed (TODO) test at t/Genewise.t line 79.
# got: 'Scaffold_2042.1'
# expected: 'SINFRUP00000067802'
# Failed (TODO) test at t/Genewise.t line 80.
# got: 'SINFRUP00000067802'
# expected: 'Scaffold_2042.1'
t/Genewise...................NOK 37/53
# Failed test at t/Genewise.t line 82.
# got: ''
# expected: '2054.68'
t/Genewise...................NOK 41/53
# Failed test at t/Genewise.t line 88.
# got: ''
# expected: '2054.68'
t/Genewise...................NOK 45/53
# Failed test at t/Genewise.t line 93.
# got: ''
# expected: '2054.68'
# Looks like you failed 3 tests of 53.
t/Genewise...................dubious
Test returned status 3 (wstat 768, 0x300)
DIED. FAILED tests 37, 41, 45
Failed 3/53 tests, 94.34% okay
t/Genomewise.................ok
t/Genpred....................ok 1/157Argument "<1" isn't numeric in numeric
gt (>) at
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/Tools/Glimmer.pm line
519, <GEN11> line 2.
t/Genpred....................ok
t/GraphAdaptor...............ok
t/GuessSeqFormat.............ok
t/HNN........................ok
t/Handler....................ok 288/545
# Failed (TODO) test at t/Handler.t line 696.
t/Handler....................ok
t/HtSNP......................ok
t/IUPAC......................ok
t/Index......................ok
t/InstanceSite...............ok
t/InterProParser.............ok
t/LargeLocatableSeq..........ok
t/LinkageMap.................ok
t/LiveSeq....................ok
t/LocatableSeq...............ok
t/Location...................ok
t/LocationFactory............ok
t/LocusLink..................ok
t/MK.........................ok
4/46 skipped: various reasons
t/Map........................ok
t/MapIO......................ok
t/Matrix.....................ok
t/MeSH.......................ok
t/Measure....................ok
t/MetaSeq....................ok
t/MicrosatelliteMarker.......ok
t/MiniMIMentry...............ok
t/MitoProt...................ok
t/Molphy.....................ok
t/MultiFile..................ok
t/Mutation...................ok
t/Mutator....................ok
t/NetPhos....................ok
t/Node.......................ok
t/OMIMentry..................ok
t/OMIMentryAllelicVariant....ok
t/OMIMparser.................ok
t/OddCodes...................ok
t/Ontology...................ok
t/OntologyEngine.............ok
t/OntologyStore..............ok
t/PAML.......................ok
t/Perl.......................ok
t/Phenotype..................ok
t/PhylipDist.................ok
t/PhysicalMap................ok
t/Pictogram..................ok
t/PodSyntax..................skipped
all skipped: Test::Pod 1.00 required for testing POD
t/PopGen.....................ok 1/99
# Failed (TODO) test at t/PopGen.t line 242.
t/PopGen.....................ok
2/99 unexpectedly succeeded
TODO PASSED tests 97-98
t/PopGenSims.................ok
t/PrimarySeq.................ok
t/Primer.....................ok
t/Promoterwise...............ok
t/ProtDist...................ok
t/ProtMatrix.................ok
t/ProtPsm....................ok
10/14 skipped: various reasons
t/Pseudowise.................ok
t/QRNA.......................ok
t/RNAChange..................ok
t/RNA_SearchIO...............ok 2/496
# Failed (TODO) test 'HSP meta'
# at t/RNA_SearchIO.t line 798.
# undef
# ne
# undef
# Failed (TODO) test at t/RNA_SearchIO.t line 800.
# undef
# ne
# undef
# Failed (TODO) test at t/RNA_SearchIO.t line 802.
# undef
# ne
# undef
# Failed (TODO) test 'HSP meta'
# at t/RNA_SearchIO.t line 848.
# undef
# ne
# undef
# Failed (TODO) test at t/RNA_SearchIO.t line 850.
# undef
# ne
# undef
# Failed (TODO) test at t/RNA_SearchIO.t line 852.
# undef
# ne
# undef
t/RNA_SearchIO...............ok
t/RandDistFunctions..........ok
t/RandomTreeFactory..........ok
t/Range......................ok
t/RangeI.....................ok
t/RefSeq.....................ok
t/Registry...................ok 1/14
--------------------- WARNING ---------------------
MSG: Couldn't call new_from_registry() on [Bio::DB::Flat]
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: you must specify an indexing scheme
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/Root/Root.pm:357
STACK: Bio::DB::Flat::new
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/DB/Flat.pm:160
STACK: Bio::DB::Flat::new_from_registry
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/DB/Flat.pm:252
STACK: Bio::DB::Registry::_load_registry
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/DB/Registry.pm:164
STACK: Bio::DB::Registry::new
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/DB/Registry.pm:95
STACK: t/Registry.t:51
-----------------------------------------------------------
---------------------------------------------------
t/Registry...................ok
6/14 skipped: various reasons
t/Relationship...............ok
t/RelationshipType...........ok
t/RemoteBlast................ok
t/RepeatMasker...............ok
t/RestrictionAnalysis........ok
t/RestrictionIO..............ok 1/15
# Failed (TODO) test at t/RestrictionIO.t line 31.
t/RestrictionIO..............ok
t/Root-Utilities.............ok 1/50
--------------------- WARNING ---------------------
MSG: Not owner of file t/data/test.txt. Compressing to temp file
/tmp/MBKEv1uzJB.tmp.bioperl.gz.
---------------------------------------------------
t/Root-Utilities.............ok
t/RootI......................ok
t/RootIO.....................ok
t/RootStorable...............ok
t/SNP........................ok
t/Scansite...................ok
5/14 skipped: various reasons
t/SearchDist.................skipped
all skipped: The optional module Bio::Ext::Align (or dependencies
thereof) was not installed
t/SearchIO...................ok 529/1449
# Failed (TODO) test at t/SearchIO.t line 989.
# '0.852'
# >
# '0.9'
# Failed (TODO) test at t/SearchIO.t line 990.
# '1.599'
# <=
# '1'
t/SearchIO...................ok
t/Seg........................ok
t/Seq........................ok
t/SeqAnalysisParser..........ok
t/SeqBuilder.................ok
t/SeqDiff....................ok
t/SeqEvolution...............ok
t/SeqFeatAnnotated...........ok
t/SeqFeatCollection..........ok
t/SeqFeature.................ok
t/SeqHound_DB................ok
t/SeqIO......................ok
t/SeqPattern.................ok
t/SeqStats...................ok
t/SeqUtils...................ok
t/SeqVersion.................ok
t/SeqWords...................ok
t/SequenceFamily.............ok
t/Sigcleave..................ok
t/Signalp....................ok
t/Signalp2...................ok
t/Sim4.......................ok
t/SimilarityPair.............ok
t/SimpleAlign................ok
t/SiteMatrix.................ok
t/Sopma......................ok
t/Species....................ok
t/Spidey.....................ok
t/StandAloneBlast............ok
11/45 skipped: various reasons
t/StructIO...................ok
t/Structure..................ok
t/Symbol.....................ok
t/TagHaplotype...............ok
t/TandemRepeatsFinder........ok
t/TaxonTree..................skipped
all skipped: All tests are being skipped, probably because the
module(s) being tested here are now deprecated
t/Taxonomy...................ok
t/Tempfile...................ok
t/Term.......................ok
t/Tmhmm......................ok
t/Tools......................ok
t/Tree.......................ok
t/TreeBuild..................ok
t/TreeIO.....................ok
t/UCSCParsers................ok
t/Unflattener................ok
t/Unflattener2...............ok
t/UniGene....................ok
t/Variation_IO...............ok
t/WABA.......................ok
t/WrapperBase................ok
t/abi........................skipped
all skipped: The optional module Bio::SeqIO::staden::read (or
dependencies thereof) was not installed
t/ace........................ok
t/alignUtilities.............ok
t/asciitree..................ok
t/blast_pull.................ok 1/287
# Failed (TODO) test at t/blast_pull.t line 258.
# got: '0.946'
# expected: '0.943'
t/blast_pull.................ok
t/bsml_sax...................ok
t/chaosxml...................ok
t/cigarstring................ok
t/consed.....................ok
t/ctf........................skipped
all skipped: The optional module Bio::SeqIO::staden::read (or
dependencies thereof) was not installed
t/dblink.....................ok
t/ePCR.......................ok
t/embl.......................ok
t/entrezgene.................ok 542/1422Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.
t/entrezgene.................ok 966/1422Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.
Pseudo-hashes are deprecated at
/home/forrest/src/bioperl/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line
491.
t/entrezgene.................ok
t/est2genome.................ok
t/exp........................skipped
all skipped: The optional module Bio::SeqIO::staden::read (or
dependencies thereof) was not installed
t/fasta......................ok
t/flat.......................ok
t/game.......................ok
t/gcg........................ok
t/genbank....................ok
t/hmmer......................ok
t/hmmer_pull.................ok
t/interpro...................ok
t/kegg.......................ok
t/largefasta.................ok
t/largepseq..................ok
t/lasergene..................ok
t/lucy.......................ok
t/masta......................ok
t/metafasta..................ok
t/multiple_fasta.............ok
t/obo_parser.................ok
t/pICalculator...............ok
t/phd........................ok
t/pir........................ok
t/pln........................skipped
all skipped: The optional module Bio::SeqIO::staden::read (or
dependencies thereof) was not installed
t/primaryqual................ok
t/primedseq..................ok
t/primer3....................ok
t/protgraph..................ok 1/70
# Failed (TODO) test at t/protgraph.t line 55.
# Failed (TODO) test at t/protgraph.t line 56.
# got: '13'
# expected: '14'
t/protgraph..................ok 49/70
# Failed (TODO) test at t/protgraph.t line 248.
# got: 'Helicobacter pylori'
# expected: 'Helicobacter pylori 26695'
t/protgraph..................ok
t/psm........................ok
t/qual.......................ok
t/raw........................ok
t/rnamotif...................ok
t/scf........................ok
t/seq_quality................ok
t/seqfeaturePrimer...........ok
t/seqread_fail...............ok
t/sequencetrace..............ok
t/seqwithquality.............ok
t/simpleGOparser.............ok
t/singlet....................ok
t/sirna......................ok
t/splicedseq.................ok
t/swiss......................ok 1/239
# Failed (TODO) test at t/swiss.t line 47.
t/swiss......................ok
t/tRNAscanSE.................ok
t/tab........................ok
t/table......................ok
t/targetp....................ok
t/tigrxml....................ok
t/tinyseq....................ok
t/trim.......................ok
t/ztr........................skipped
all skipped: The optional module Bio::SeqIO::staden::read (or
dependencies thereof) was not installed
Failed Test Stat Wstat Total Fail List of Failed
----------------------------------------------------------------------------
---
t/Assembly.t 1 256 35 1 31
t/Genewise.t 3 768 53 3 37 41 45
(3 subtests UNEXPECTEDLY SUCCEEDED), 9 tests and 43 subtests skipped.
Failed 2/248 test scripts. 4/15415 subtests failed.
Files=248, Tests=15415, 973 wallclock secs (123.75 cusr + 8.58 csys =
132.33 CPU)
Failed 2/248 test programs. 4/15415 subtests failed.
-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Friday, September 28, 2007 1:00 PM
To: Forrest Zhang
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] load_seqdatabase.pl error
If this is occurring using bioperl from CVS then I'll try taking a
look at it.
chris
On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
> Hilmar,
> I have already pre-loaded the NCBI taxonomy using
> load_ncbi_taxonomy.pl yet. The error message show:
>
> --------------------- WARNING ---------------------
> MSG: The supplied lineage does not start near 'Phaseolus aureus' (I
> was
> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
> | rosids
> | core eudicotyledons | eudicotyledons | Magnoliophyta |
> Euphyllophyta |
> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
> ---------------------------------------------------
> Could not store Q40784:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Species) failed to insert or to be found
> by unique
> key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::Persistent::PersistentObject::create
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
> PersistentObject.pm:244
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:169
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
> PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:633
> -----------------------------------------------------------
> Sigh~~~~~~
>
> Forrest Zhang
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Friday, September 28, 2007 6:17 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest,
>
> have you preloaded the NCBI taxonomy as suggested in the BioSQL
> installation guidelines? SwissProt format has NCBI taxon IDs, and the
> code will try to use it to look up species and their lineage, rather
> than inserting the lineage from whatever BioPerl parses out of the
> sequence record.
>
> -hilmar
>
> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>
>> Hi, all
>> I install the biosql, and bioperl-db. I want to import
>> swissport data.
>> But the programe show some error as below:
>> =====================================================================
>> =
>> ======
>> ===============================================
>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver mysql
>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>> Could not store Q6DAH5:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>> subsp.
>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>> Pectobacterium |
>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>> Proteobacteria | Bacteria')
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>> STACK: Bio::Species::classification
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>> PersistentObject.pm:552
>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:1305
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:973
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:852
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:182
>> STACK: Bio::DB::Persistent::PersistentObject::create
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>> PersistentObject.pm:244
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:169
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:251
>> STACK: Bio::DB::Persistent::PersistentObject::store
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>> PersistentObject.pm:271
>> STACK: load_seqdatabase.pl:620
>> -----------------------------------------------------------
>>
>> at load_seqdatabase.pl line 633
>> =====================================================================
>> =
>> ======
>> ===============================================
>>
>> How can I solve it, please help me, Thank you.
>>
>> Thanks
>> Forrest zhang
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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