[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Chris Fields cjfields at illinois.edu
Sun Jan 18 00:07:09 EST 2009


Brian,

Okay, I see what's wrong with the phyloxml tests, have fixed it (some  
leftover cruft).  Thanks for pointing that one out!

I had some problems with the latest version of io_lib myself but only  
with abi.t.  ABI and ALF formats do not come with io_lib anymore (I  
think they are still included in the staden lib download, though).   
For some reason we have a test suite for Bio::SeqIO::alf but  
apparently no test data!

chris

On Jan 17, 2009, at 9:05 PM, Brian Osborne wrote:

> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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