[Bioperl-l] Bioperl 1.5.2 RC1

Phillip San Miguel pmiguel at purdue.edu
Wed Oct 4 15:38:51 EDT 2006


Sendu Bala wrote:
> Bioperl 1.5.2 Release Candidate 1 is ready and available in CVS. I'll 
> upload tar.gz files when I have access to the server, then reply here 
> with links.
>
> In the mean time, see http://www.bioperl.org/wiki/Release_1.5.2 for 
> instructions on getting and testing this RC.
>
> Developers:
>    Make sure you're in the AUTHORS file in all 4 packages, as
>    appropriate.
>
> Users:
>    Even though 1.5.2 is a 'developer' release, we consider it the most
>    stable and capable version of Bioperl, and recommend that you use
>    it in all but the most critical production environments. Please
>    try it out and let us know of any problems or difficulties you run
>    into.
>
>
> Thank you,
> Sendu.
>   
I didn't see any tests done under solaris, so I asked our sys admin to 
do the install on one of our machines.

Just another data point:

He installed this release candidate on a Sun E450 box running solaris. 
uname -a gives:

SunOS descartes 5.10 Generic_118833-18 sun4u sparc SUNW,Ultra-4

perl -v gives:

This is perl, v5.8.8 built for sun4-solaris
(etc.)


$ time make test
PERL_DL_NONLAZY=1 /usr/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/AAChange...................ok
t/AAReverseMutate............ok
t/abi........................Bio::SeqIO::staden::read from bioperl-ext is not installed or is installed incorrectly - skipping abi.t tests
t/abi........................ok
t/ace........................ok
t/AlignIO....................ok
t/AlignStats.................ok
t/AlignUtil..................ok
t/alignUtilities.............ok
t/Allele.....................ok
t/Alphabet...................ok
t/Annotation.................ok
t/AnnotationAdaptor..........ok
t/asciitree..................ok
t/Assembly...................ok
        1/19 skipped:
t/Biblio.....................ok
t/Biblio_biofetch............ok
t/Biblio_eutils..............ok
t/BiblioReferences...........ok
t/BioDBGFF...................ok
t/BioDBSeqFeature............ok 1/46Argument "+" isn't numeric in numeric lt (<) at Bio/DB/SeqFeature/Segment.pm line 423.
t/BioDBSeqFeature............ok
t/BioDBSeqFeature_BDB........ok
t/BioDBSeqFeature_mysql......ok 3/46prepare_cached(SELECT max(offset) FROM sequence as s,locationlist as ll WHERE s.id=ll.id AND ll.seqname=? AND offset<=?) statement handle DBI::st=HASH(0x8c5258) still Active at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1422
prepare_cached(SELECT max(offset) FROM sequence as s,locationlist as ll WHERE s.id=ll.id AND ll.seqname=? AND offset<=?) statement handle DBI::st=HASH(0x8c5258) still Active at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1422
prepare_cached(SELECT max(offset) FROM sequence as s,locationlist as ll WHERE s.id=ll.id AND ll.seqname=? AND offset<=?) statement handle DBI::st=HASH(0x8c5258) still Active at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1422
prepare_cached(SELECT sequence,offset
   FROM sequence as s,locationlist as ll
   WHERE s.id=ll.id
     AND ll.seqname= ?
     AND offset >= ?
     AND offset <= ?
   ORDER BY offset
) statement handle DBI::st=HASH(0x8c5048) still Active at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1422
prepare_cached(SELECT max(offset) FROM sequence as s,locationlist as ll WHERE s.id=ll.id AND ll.seqname=? AND offset<=?) statement handle DBI::st=HASH(0x8c5258) still Active at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1422
prepare_cached(SELECT sequence,offset
   FROM sequence as s,locationlist as ll
   WHERE s.id=ll.id
     AND ll.seqname= ?
     AND offset >= ?
     AND offset <= ?
   ORDER BY offset
) statement handle DBI::st=HASH(0x8c5048) still Active at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1422
t/BioDBSeqFeature_mysql......ok
t/BioFetch_DB................ok
t/BioGraphics................ok
t/BlastIndex.................ok 1/13
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BlastIndex.................ok
t/BPbl2seq...................
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPbl2seq is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BPbl2seq...................ok 1/108
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPbl2seq is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPbl2seq is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPbl2seq is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPbl2seq is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BPbl2seq...................ok
t/BPlite.....................ok 1/97
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BPlite.....................ok 52/97
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BPlite.....................ok 88/97
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
STACK Bio::Tools::BPlite::new /usr/local/src/bioperl-1.5.2-RC1/bioperl-1.5.2-RC1/blib/lib/Bio/Tools/BPlite.pm:197
STACK toplevel t/BPlite.t:127

-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPlite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BPlite.....................ok
t/BPpsilite..................
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPpsilite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BPpsilite..................ok 4/11
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::BPpsilite is deprecatedUse Bio::SearchIO classes instead
---------------------------------------------------
t/BPpsilite..................ok
t/bsml_sax...................ok
t/Chain......................ok
t/chaosxml...................ok
t/cigarstring................ok
t/ClusterIO..................ok
t/Coalescent.................ok
t/CodonTable.................ok
t/Compatible.................ok
t/consed.....................ok
t/CoordinateGraph............ok
t/CoordinateMapper...........ok
t/Correlate..................ok
t/ctf........................Bio::SeqIO::staden::read of bioperl-ext is not installed or is installed incorrectly - skipping ctf.t tests
t/ctf........................ok
t/CytoMap....................ok
t/DB.........................skipped
        all skipped: Skipping all tests since they require network access, set BIOPERLDEBUG=1 to test
t/DBCUTG.....................ok
        11/34 skipped: Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
t/DBFasta....................ok
t/DNAMutation................ok
t/Domcut.....................ok
t/ECnumber...................ok
t/ELM........................ok 1/13
-------------------- WARNING ---------------------
MSG: sleeping for 1 seconds

---------------------------------------------------
t/ELM........................ok
t/embl.......................ok
t/EMBL_DB....................ok
t/EMBOSS_Tools...............ok
t/EncodedSeq.................ok
t/entrezgene.................ok 491/1003Pseudo-hashes are deprecated at /usr/local/src/bioperl-1.5.2-RC1/bioperl-1.5.2-RC1/blib/lib/Bio/SeqIO/entrezgene.pm line 467.
t/entrezgene.................ok 695/1003Pseudo-hashes are deprecated at /usr/local/src/bioperl-1.5.2-RC1/bioperl-1.5.2-RC1/blib/lib/Bio/SeqIO/entrezgene.pm line 467.
t/entrezgene.................ok 723/1003Pseudo-hashes are deprecated at /usr/local/src/bioperl-1.5.2-RC1/bioperl-1.5.2-RC1/blib/lib/Bio/SeqIO/entrezgene.pm line 467.
t/entrezgene.................ok 824/1003Pseudo-hashes are deprecated at /usr/local/src/bioperl-1.5.2-RC1/bioperl-1.5.2-RC1/blib/lib/Bio/SeqIO/entrezgene.pm line 467.
t/entrezgene.................ok
t/ePCR.......................ok
t/ESEfinder..................ok 1/15# Looks like you planned 15 tests but only ran 14.
t/ESEfinder..................dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED test 15
        Failed 1/15 tests, 93.33% okay (less 9 skipped tests: 5 okay, 33.33%)
t/est2genome.................ok
t/EUtilities.................skipped
        all skipped: Set BIOPERLDEBUG=1 to run tests
t/Exception..................ok
t/Exonerate..................ok
t/exp........................Bio::SeqIO::staden::read of bioperl-ext is not installed or is installed incorrectly - skipping exp.t tests
t/exp........................ok
t/fasta......................ok
t/FeatureIO..................ok 7/33
-------------------- WARNING ---------------------
MSG: '##feature-ontology' directive handling not yet implemented
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: '##attribute-ontology' directive handling not yet implemented
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: '##source-ontology' directive handling not yet implemented
---------------------------------------------------
t/FeatureIO..................ok
t/flat.......................ok
t/FootPrinter................ok
t/game.......................ok
t/GbrowseGFF.................ok
t/gcg........................ok
t/GDB........................ok
t/Gel........................ok
t/genbank....................ok
t/GeneCoordinateMapper.......ok
t/Geneid.....................ok
t/Genewise...................ok
        2/51 skipped:
t/Genomewise.................ok
t/Genpred....................ok
t/GFF........................ok
t/GOR4.......................ok
t/GOterm.....................ok
t/GraphAdaptor...............ok
t/GuessSeqFormat.............ok
t/hmmer......................ok
t/hmmer_pull.................ok
t/HNN........................ok
t/HtSNP......................ok
t/Index......................ok
t/InstanceSite...............ok
t/interpro...................ok
t/InterProParser.............ok
t/IUPAC......................ok
t/kegg.......................ok
t/largefasta.................ok
t/LargeLocatableSeq..........ok
t/largepseq..................ok
t/lasergene..................ok
t/LinkageMap.................ok
t/LiveSeq....................ok
t/LocatableSeq...............ok
t/Location...................ok
t/LocationFactory............ok
t/LocusLink..................ok
t/lucy.......................ok
t/Map........................ok
t/MapIO......................ok
t/masta......................ok
t/Matrix.....................ok
t/Measure....................ok
t/MeSH.......................ok
t/metafasta..................ok
t/MetaSeq....................ok
t/MicrosatelliteMarker.......ok
t/MiniMIMentry...............ok
t/MitoProt...................ok
t/Molphy.....................ok
t/MultiFile..................ok
t/multiple_fasta.............ok
t/Mutation...................ok
t/Mutator....................ok
t/NetPhos....................ok
        10/14 skipped: Skipping tests which require network access, set BIOPERLDEBUG=1 to test
t/Node.......................ok
t/obo_parser.................ok
t/OddCodes...................ok
t/OMIMentry..................ok
t/OMIMentryAllelicVariant....ok
t/OMIMparser.................ok
t/Ontology...................ok
t/OntologyEngine.............ok
t/OntologyStore..............ok
t/PAML.......................ok
t/Perl.......................ok
t/phd........................ok
t/Phenotype..................ok
t/PhylipDist.................ok
t/PhysicalMap................ok
t/pICalculator...............ok
t/Pictogram..................ok
t/pir........................ok
t/pln........................Bio::SeqIO::staden::read of bioperl-ext is not installed or is installed incorrectly - skipping pln.t tests
t/pln........................ok
t/PopGen.....................ok
        2/89 skipped:
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/protgraph..................ok
t/ProtMatrix.................ok
t/ProtPsm....................ok
t/Pseudowise.................ok
t/psm........................ok
t/QRNA.......................ok
t/qual.......................ok
t/RandDistFunctions..........ok
t/RandomTreeFactory..........ok
t/Range......................ok
t/RangeI.....................ok
t/raw........................ok
t/RefSeq.....................ok
t/Registry...................ok
t/Relationship...............ok
t/RelationshipType...........ok
t/RemoteBlast................ok
        11/13 skipped: to avoid timeout
t/RepeatMasker...............ok
t/RestrictionAnalysis........ok
t/RestrictionEnzyme..........ok 1/14
-------------------- WARNING ---------------------
MSG: Use of Bio::Tools::RestrictionEnzyme is deprecatedUse Bio::Restriction classes instead
---------------------------------------------------
t/RestrictionEnzyme..........ok
t/RestrictionIO..............ok
t/RNAChange..................ok
t/rnamotif...................ok
t/RootI......................ok
t/RootIO.....................ok
        2/27 skipped: various reasons
t/RootStorable...............ok
t/Scansite...................ok
t/scf........................ok
t/SearchDist.................ok
t/SearchIO...................ok
t/Seg........................ok
t/Seq........................ok
t/seq_quality................ok
t/SeqAnalysisParser..........ok
t/SeqBuilder.................ok
t/SeqDiff....................ok
t/SeqFeatCollection..........ok
t/SeqFeature.................ok
t/seqfeaturePrimer...........ok
t/SeqHound_DB................ok 4/14Writing into 'shoundlog' log file.
t/SeqHound_DB................ok
t/SeqIO......................ok
t/SeqPattern.................ok
t/seqread_fail...............ok
t/SeqStats...................ok
t/SequenceFamily.............ok
t/sequencetrace..............ok
t/SeqUtils...................ok
t/SeqVersion.................ok
t/seqwithquality.............ok
t/SeqWords...................ok
t/Sigcleave..................ok
t/Signalp....................ok
t/Sim4.......................ok
t/SimilarityPair.............ok
t/SimpleAlign................ok
t/simpleGOparser.............ok
t/singlet....................ok
t/sirna......................ok
t/SiteMatrix.................ok
t/SNP........................ok
t/Sopma......................ok
t/Species....................ok
        5/20 skipped: Skipping tests which require network access, set BIOPERLDEBUG=1 to test
t/Spidey.....................ok
t/splicedseq.................ok
t/StandAloneBlast............ok
t/StructIO...................ok
t/Structure..................ok
t/swiss......................ok
t/Symbol.....................ok
t/tab........................ok
t/table......................ok
t/TagHaplotype...............ok
t/Taxonomy...................ok
        44/98 skipped: Skipping tests which require network access, set BIOPERLDEBUG=1 to test
t/TaxonTree..................ok
t/Tempfile...................ok
t/Term.......................ok
t/tigrxml....................ok
t/tinyseq....................ok
t/Tmhmm......................ok
t/Tools......................ok
t/Tree.......................ok
t/TreeBuild..................ok
t/TreeIO.....................ok
t/trim.......................ok
t/tRNAscanSE.................ok
t/UCSCParsers................ok
t/Unflattener................ok
t/Unflattener2...............ok
t/UniGene....................ok
t/Variation_IO...............ok
t/WABA.......................ok
t/XEMBL_DB...................ok
        1/9 skipped: server may be down
t/ztr........................Bio::SeqIO::staden::read of bioperl-ext is not installed or is installed incorrectly - skipping ztr.t tests
t/ztr........................ok
Failed Test   Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/ESEfinder.t  255 65280    15    2  13.33%  15
2 tests and 98 subtests skipped.
Failed 1/240 test scripts, 99.58% okay. 1/11910 subtests failed, 99.99% okay.
*** Error code 29
make: Fatal error: Command failed for target `test_dynamic'

real    13m10.064s
user    11m14.891s
sys     0m45.417s

$ TEST_VERBOSE=1 perl t/ESEfinder.t
1..15
ok 1 - use Bio::Tools::Analysis::DNA::ESEfinder;
ok 2 - use Data::Dumper;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::Seq;
ok 5
ok 6 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 7 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 8 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 9 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 10 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 11 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 12 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 13 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
ok 14 # skip Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test
# Looks like you planned 15 tests but only ran 14.






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