[Bioperl-l] FW: load_seqdatabase.pl error

Forrest Zhang forrest_zhang at 163.com
Fri Sep 28 01:34:21 EDT 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








More information about the Bioperl-l mailing list