[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3
Brian Osborne
bosborne11 at verizon.net
Sun Jan 18 03:05:23 UTC 2009
Chris,
Looks good. I do see a bunch of errors concerning the modules that use
the Staden library. It looks like I have some older Staden library on
my laptop, "wrong architecture". Not sure how you want to deal with
that but I'd say that this is not the fault of Bioperl.
The second issue is this:
t/Tree/TreeIO/phyloxml.........................You tried to plan
twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17
BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22.
# Looks like your test died before it could output anything.
t/Tree/TreeIO/phyloxml......................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 97/97 subtests
Perl:
This is perl, v5.8.8 built for darwin-thread-multi-2level
(with 1 registered patch, see perl -V for more detail)
Test Summary Report
-------------------
t/SeqIO/abi.t (Wstat: 65280 Tests: 1
Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 7 tests but ran 1.
t/SeqIO/alf.t (Wstat: 65280 Tests: 1
Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 8 tests but ran 1.
t/SeqIO/ctf.t (Wstat: 65280 Tests: 1
Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 4 tests but ran 1.
t/SeqIO/exp.t (Wstat: 65280 Tests: 1
Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 3 tests but ran 1.
t/SeqIO/pln.t (Wstat: 65280 Tests: 1
Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 4 tests but ran 1.
t/SeqIO/ztr.t (Wstat: 65280 Tests: 1
Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 3 tests but ran 1.
t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0
Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 97 tests but ran 0.
Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys +
109.70 cusr 15.28 csys = 129.60 CPU)
Result: FAIL
Failed 7/318 test programs. 0/17997 subtests failed.
Brian O.
t/SeqIO/abi....................................1/7 Had problems
bootstrapping Inline module 'Bio::SeqIO::staden::read'
Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/
SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read:
dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/
staden/read/read.bundle, 1): no suitable image found. Did find:
/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/
read/read.bundle: mach-o, but wrong architecture at /System/Library/
Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, <DATA>
line 1.
at /Library/Perl/5.8.6/Inline.pm line 500
at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/
DynaLoader.pm line 0
INIT failed--call queue aborted, <DATA> line 1.
# Looks like you planned 7 tests but only ran 1.
# Looks like your test died just after 1.
t/SeqIO/abi.................................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 6/7 subtests
t/SeqIO/ace....................................ok
t/SeqIO/agave..................................ok
t/SeqIO/alf....................................1/8 Had problems
bootstrapping Inline module 'Bio::SeqIO::staden::read'
Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/
SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read:
dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/
staden/read/read.bundle, 1): no suitable image found. Did find:
/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/
read/read.bundle: mach-o, but wrong architecture at /System/Library/
Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, <DATA>
line 1.
at /Library/Perl/5.8.6/Inline.pm line 500
at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/
DynaLoader.pm line 0
INIT failed--call queue aborted, <DATA> line 1.
# Looks like you planned 8 tests but only ran 1.
# Looks like your test died just after 1.
t/SeqIO/alf.................................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 7/8 subtests
t/SeqIO/asciitree..............................ok
t/SeqIO/bsml...................................ok
t/SeqIO/bsml_sax...............................skipped: The optional
module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/chadoxml...............................ok
t/SeqIO/chaos..................................ok
t/SeqIO/chaosxml...............................ok
t/SeqIO/ctf....................................1/4 Had problems
bootstrapping Inline module 'Bio::SeqIO::staden::read'
Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/
SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read:
dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/
staden/read/read.bundle, 1): no suitable image found. Did find:
/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/
read/read.bundle: mach-o, but wrong architecture at /System/Library/
Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, <DATA>
line 1.
at /Library/Perl/5.8.6/Inline.pm line 500
at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/
DynaLoader.pm line 0
INIT failed--call queue aborted, <DATA> line 1.
# Looks like you planned 4 tests but only ran 1.
# Looks like your test died just after 1.
t/SeqIO/ctf.................................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 3/4 subtests
t/SeqIO/embl...................................ok
t/SeqIO/entrezgene.............................skipped: The optional
module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel..................................ok
t/SeqIO/exp....................................1/3 Had problems
bootstrapping Inline module 'Bio::SeqIO::staden::read'
Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/
SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read:
dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/
staden/read/read.bundle, 1): no suitable image found. Did find:
/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/
read/read.bundle: mach-o, but wrong architecture at /System/Library/
Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, <DATA>
line 1.
at /Library/Perl/5.8.6/Inline.pm line 500
at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/
DynaLoader.pm line 0
INIT failed--call queue aborted, <DATA> line 1.
# Looks like you planned 3 tests but only ran 1.
# Looks like your test died just after 1.
t/SeqIO/exp.................................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 2/3 subtests
t/SeqIO/fasta..................................ok
t/SeqIO/fastq..................................ok
t/SeqIO/flybase_chadoxml.......................ok
t/SeqIO/game...................................ok
t/SeqIO/gcg....................................1/17
# Failed (TODO) test 'primary_id'
# in t/SeqIO/gcg.t at line 54.
# got: 'Bio::PrimarySeq=HASH(0x97fe30)'
# expected: 'roa1_drome'
t/SeqIO/gcg....................................ok
t/SeqIO/genbank................................ok
t/SeqIO/interpro...............................ok
t/SeqIO/kegg...................................ok
t/SeqIO/largefasta.............................ok
t/SeqIO/lasergene..............................ok
t/SeqIO/locuslink..............................ok
t/SeqIO/metafasta..............................ok
t/SeqIO/phd....................................ok
t/SeqIO/pir....................................ok
t/SeqIO/pln....................................1/4 Had problems
bootstrapping Inline module 'Bio::SeqIO::staden::read'
Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/
SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read:
dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/
staden/read/read.bundle, 1): no suitable image found. Did find:
/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/
read/read.bundle: mach-o, but wrong architecture at /System/Library/
Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, <DATA>
line 1.
at /Library/Perl/5.8.6/Inline.pm line 500
at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/
DynaLoader.pm line 0
INIT failed--call queue aborted, <DATA> line 1.
# Looks like you planned 4 tests but only ran 1.
# Looks like your test died just after 1.
t/SeqIO/pln.................................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 3/4 subtests
t/SeqIO/qual...................................ok
t/SeqIO/raw....................................ok
t/SeqIO/scf....................................1/59
# Failed (TODO) test 'accuracies'
# in t/SeqIO/scf.t at line 78.
# got: 'ARRAY(0x995314)'
# expected: '482'
t/SeqIO/scf....................................ok
t/SeqIO/strider................................skipped: The optional
module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/swiss..................................ok
t/SeqIO/tab....................................ok
t/SeqIO/table..................................ok
t/SeqIO/tigr...................................ok
t/SeqIO/tigrxml................................skipped: The optional
module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/tinyseq................................ok
t/SeqIO/ztr....................................1/3 Had problems
bootstrapping Inline module 'Bio::SeqIO::staden::read'
Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/
SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read:
dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/
staden/read/read.bundle, 1): no suitable image found. Did find:
/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/
read/read.bundle: mach-o, but wrong architecture at /System/Library/
Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, <DATA>
line 1.
at /Library/Perl/5.8.6/Inline.pm line 500
at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/
DynaLoader.pm line 0
INIT failed--call queue aborted, <DATA> line 1.
# Looks like you planned 3 tests but only ran 1.
# Looks like your test died just after 1.
t/SeqIO/ztr.................................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 2/3 subtests
t/SeqTools/CodonTable..........................ok
t/SeqTools/ECnumber............................ok
t/SeqTools/GuessSeqFormat......................ok
t/SeqTools/OddCodes............................ok
t/SeqTools/SeqPattern..........................ok
t/SeqTools/SeqStats............................ok
t/SeqTools/SeqUtils............................ok
t/SeqTools/SeqWords............................ok
t/Species......................................ok
t/Structure/IO.................................ok
t/Structure/Structure..........................ok
t/Symbol.......................................ok
t/TaxonTree....................................skipped: All tests are
being skipped, probably because the module(s) being tested here are
now deprecated
t/Tools/Alignment/Consed.......................ok
t/Tools/Analysis/DNA/ESEfinder.................skipped: Network tests
have not been requested
t/Tools/Analysis/Protein/Domcut................skipped: Network tests
have not been requested
t/Tools/Analysis/Protein/ELM...................skipped: Network tests
have not been requested
t/Tools/Analysis/Protein/GOR4..................skipped: Network tests
have not been requested
t/Tools/Analysis/Protein/HNN...................skipped: Network tests
have not been requested
t/Tools/Analysis/Protein/Mitoprot..............skipped: Network tests
have not been requested
t/Tools/Analysis/Protein/NetPhos...............skipped: Network tests
have not been requested
t/Tools/Analysis/Protein/Scansite..............ok
t/Tools/Analysis/Protein/Sopma.................ok
t/Tools/EMBOSS/Palindrome......................ok
t/Tools/EUtilities/EUtilParameters.............ok
t/Tools/EUtilities/egquery.....................ok
t/Tools/EUtilities/einfo.......................ok
t/Tools/EUtilities/elink_acheck................ok
t/Tools/EUtilities/elink_lcheck................ok
t/Tools/EUtilities/elink_llinks................ok
t/Tools/EUtilities/elink_ncheck................ok
t/Tools/EUtilities/elink_neighbor..............ok
t/Tools/EUtilities/elink_neighbor_history......ok
t/Tools/EUtilities/elink_scores................ok
t/Tools/EUtilities/epost.......................ok
t/Tools/EUtilities/esearch.....................ok
t/Tools/EUtilities/espell......................ok
t/Tools/EUtilities/esummary....................ok
t/Tools/Est2Genome.............................ok
t/Tools/FootPrinter............................ok
t/Tools/GFF....................................ok
t/Tools/Geneid.................................ok
t/Tools/Genewise...............................ok
t/Tools/Genomewise.............................ok
t/Tools/Genpred................................ok
t/Tools/Hmmer..................................ok
t/Tools/IUPAC..................................ok
t/Tools/Lucy...................................ok
t/Tools/Match..................................ok
t/Tools/Phylo/Gerp.............................ok
t/Tools/Phylo/Molphy...........................ok
t/Tools/Phylo/PAML.............................ok
t/Tools/Phylo/Phylip/ProtDist..................ok
t/Tools/Primer3................................ok
t/Tools/Promoterwise...........................ok
t/Tools/Pseudowise.............................ok
t/Tools/QRNA...................................ok
t/Tools/RandDistFunctions......................ok
t/Tools/RepeatMasker...........................ok
t/Tools/Run/RemoteBlast........................skipped: Network tests
have not been requested
t/Tools/Run/StandAloneBlast....................ok
t/Tools/Run/WrapperBase........................ok
t/Tools/Seg....................................ok
t/Tools/SiRNA..................................ok
t/Tools/Sigcleave..............................ok
t/Tools/Signalp................................ok
t/Tools/Signalp/ExtendedSignalp................ok
t/Tools/Sim4...................................ok
t/Tools/Spidey/Spidey..........................ok
t/Tools/TandemRepeatsFinder....................ok
t/Tools/TargetP................................ok
t/Tools/Tmhmm..................................ok
t/Tools/ePCR...................................ok
t/Tools/pICalculator...........................ok
t/Tools/rnamotif...............................skipped: All tests are
being skipped, probably because the module(s) being tested here are
now deprecated
t/Tools/tRNAscanSE.............................ok
t/Tree/Compatible..............................ok
t/Tree/Node....................................ok
t/Tree/PhyloNetwork/Factory....................ok
t/Tree/PhyloNetwork/GraphViz...................ok
t/Tree/PhyloNetwork/MuVector...................ok
t/Tree/PhyloNetwork/PhyloNetwork...............ok
t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional
module Math::Random (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory................ok
t/Tree/RandomTreeFactory.......................ok
t/Tree/Tree....................................ok
t/Tree/TreeIO..................................ok
t/Tree/TreeIO/lintree..........................ok
t/Tree/TreeIO/newick...........................ok
t/Tree/TreeIO/nexus............................ok
t/Tree/TreeIO/nhx..............................ok
t/Tree/TreeIO/phyloxml.........................You tried to plan
twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17
BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22.
# Looks like your test died before it could output anything.
t/Tree/TreeIO/phyloxml......................... Dubious, test returned
255 (wstat 65280, 0xff00)
Failed 97/97 subtests
t/Tree/TreeIO/svggraph.........................1/4 Use of
uninitialized value in join or string at /Library/Perl/5.8.6/SVG/
Element.pm line 1169, <GEN0> line 1.
t/Tree/TreeIO/svggraph.........................ok
t/Tree/TreeIO/tabtree..........................ok
t/Tree/TreeStatistics..........................ok
t/Variation/AAChange...........................ok
t/Variation/AAReverseMutate....................ok
t/Variation/Allele.............................ok
t/Variation/DNAMutation........................ok
t/Variation/RNAChange..........................ok
t/Variation/SNP................................ok
t/Variation/SeqDiff............................ok
t/Variation/Variation_IO.......................ok
On Jan 16, 2009, at 2:11 PM, Chris Fields wrote:
> All,
>
> I would like to announce that the third (and hopefully final)
> release candidate for BioPerl 1.6 is now available for testing. As
> this is likely the final release candidate, any errors encountered
> during regression tests would be greatly appreciated.
>
> A quick note on versioning: due to issues with alpha numbered
> versions on CPAN possibly overwriting or taking precedence over a
> stable release, this release candidate has a VERSION of 1.005009_003
> (or 1.005009003). This will be switched to 1.006000 (no alpha) once
> the release is final.
>
> The RC is currently being uploaded to CPAN and should be available
> in the next 24-48 hours under authorname CJFIELDS. In the meantime,
> the release candidates can be directly downloaded here:
>
> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2
> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz
> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip
>
> Signature file:
> http://bioperl.org/DIST/SIGNATURES.md5
>
> A preliminary ActiveState PPM is also available and is located in
> the BioPerl Release Candidate repository; the directions for
> installation are here:
>
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> Please feel free to report issues with testing, installation, etc.
> on the mail list and on this page:
>
> http://www.bioperl.org/wiki/Release_1.6_Testing
>
> Again, just to note we will be releasing bioperl-run, bioperl-db,
> bioperl-network, and others separately once the final 1.6 release is
> complete.
>
> Since the last release:
>
> Fixes:
>
> 1) Remote database tests are now a bit more robust.
> 2) Bio::DB::GDB and related tests have been deprecated and removed
> (GDB is no longer available).
> 3) More warnings and test failures (via CPAN Testers) now fixed.
> 4) BLAST-related file and parsing issues resolved (per Scott Markel).
> 5) Small test fixes.
>
> Known Issues:
>
> 1) Warnings for Bio::Assembly tests are for incomplete phrap
> parsing. These modules will be a focus of BioPerl 1.7; in the
> meantime I'll see about quenching the tests.
> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to
> the latest Data::Stag (this is NOT a required upgrade).
> 3) PPM issues; note this is not high on our priority list ATM but I
> will try to address it for the next release.
> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with
> SVG::Graph.
>
> Enjoy!
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
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