February 2010 Archives by thread

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Starting: Mon Feb 1 08:45:46 EST 2010
Ending: Fri Feb 26 00:13:31 EST 2010
Messages: 110

• [Bioperl-guts-l] [Bug 3005] New: SearchIO::Blast fails to parse result produces from ncbi url-api   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3005] SearchIO::Blast fails to parse result produces from ncbi url-api   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3005] SearchIO::Blast fails to parse result produces from ncbi url-api   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3003] Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3003] Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16805] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus.pm: File:: Temp::filename is full path--fix   Mark Allen Jensen
• [Bioperl-guts-l] [16806] Bio-FeatureIO/trunk/Build.PL: tweaked and tidied Build.PL, adding pointer to repository, create_license   Robert Buels
• [Bioperl-guts-l] [16807] bioperl-dev/trunk/Bio/Tools: dev changes assoc w/WrapperMaker   Mark Allen Jensen
• [Bioperl-guts-l] [16808] bioperl-dev/trunk/Bio/Tools/WrapperMaker.pm: exporting wrapper object   Mark Allen Jensen
• [Bioperl-guts-l] [16809] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: schema tweaks and additions   Mark Allen Jensen
• [Bioperl-guts-l] [16810] bioperl-dev/trunk/Bio/Tools: pod build-out, various fixes   Mark Allen Jensen
• [Bioperl-guts-l] [16811] bioperl-dev/trunk/Bio/Tools: more WrapperMaker/ CommandExts crosstalk   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2977] TreeIO problems   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16812] bioperl-dev/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: adding self options functionality; tightening   Mark Allen Jensen
• [Bioperl-guts-l] [16813] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: small xsd refactoring and coresponding xml handling   Mark Allen Jensen
• [Bioperl-guts-l] [16814] bioperl-dev/trunk/Bio/Tools/Run/WrapperBase.pm: adding ordered hashes via Tie:IxHash, if available ( silently skips it if not)   Mark Allen Jensen
• [Bioperl-guts-l] [16815] bioperl-dev/trunk/Bio/Tools: refactoring CommandExts to handle self options   Mark Allen Jensen
• [Bioperl-guts-l] [16816] bioperl-dev/trunk/t: tests for WrapperMaker   Mark Allen Jensen
• [Bioperl-guts-l] [16817] bioperl-dev/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: tweak   Mark Allen Jensen
• [Bioperl-guts-l] [16818] bioperl-dev/trunk: tweaks to accommodate BlastPlus.pm   Mark Allen Jensen
• [Bioperl-guts-l] [16819] bioperl-dev/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: propset   Mark Allen Jensen
• [Bioperl-guts-l] [16820] bioperl-dev/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: working on integrating CommandExts refactor with existing client code ( SABlast+, Bowtie)   Mark Allen Jensen
• [Bioperl-guts-l] [16821] bioperl-dev/trunk: bug squish/test tweak   Mark Allen Jensen
• [Bioperl-guts-l] [16822] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm : yikes--this was a baddie.   Mark Allen Jensen
• [Bioperl-guts-l] [16823] bioperl-live/trunk/Bio/Root/Test.pm: export done_testing if it is present (shouldn' t use this in final tests until we upgrade the lib version, but it is awfully convenient)   Christopher John Fields
• [Bioperl-guts-l] [16824] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: metadata element   Mark Allen Jensen
• [Bioperl-guts-l] [16825] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: reagt.   Mark Allen Jensen
• [Bioperl-guts-l] [16826] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: tweak   Mark Allen Jensen
• [Bioperl-guts-l] [16827] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: doh. must be late   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 3007] New: Bio::TreeIO::nhx cannot parse empty [&&NHX] + round-trip failure   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3007] Bio::TreeIO::nhx cannot parse empty [&&NHX] + round-trip failure   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16828] bioperl-live/trunk/t/Root/RootIO.t: fixed Bio::RootIO test count   Robert Buels
• [Bioperl-guts-l] [16829] bioperl-run/trunk/lib/Bio/Tools/Run: ease off on throws; let bl2seq work without a db being specified (as it should)   Mark Allen Jensen
• [Bioperl-guts-l] [16830] bioperl-live/trunk: added some Bio::Root::IO tests for using File:: Temp filehandles, skipping if File:: Temp does not have the object-oriented interface.   Robert Buels
• [Bioperl-guts-l] [16831] bioperl-live/trunk/t/Assembly/Assembly.t: Make bowtie test skip if no Bio::Tools::Run::Samtools available (i.e.   Dan Kortschak
• [Bioperl-guts-l] [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?   Mark A. Jensen
  • [Bioperl-guts-l] [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?   Dan Kortschak
    • [Bioperl-guts-l] [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?   Mark A. Jensen
      • [Bioperl-guts-l] [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?   Dan Kortschak
• [Bioperl-guts-l] [Bug 3008] New: Bio::TreeIO::nhx cannot parse empty [&&NHX] + round-trip failure   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3008] Bio::TreeIO::nhx cannot parse empty [&&NHX] + round-trip failure   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16832] bioperl-live/trunk/t/Assembly/Assembly.t: removed strange orphan arrays; eliminated some bad tests ( to be replaced by good tests!)   Mark Allen Jensen
• [Bioperl-guts-l] [16833] Bio-FeatureIO/trunk/README: add a few comments   Christopher John Fields
• [Bioperl-guts-l] [16834] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus/ BlastMethods.pm: handle multiple results: next_result, rewind_results   Mark Allen Jensen
  • [Bioperl-guts-l] [16834] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus/ BlastMethods.pm: handle multiple results: next_result, rewind_results   Chris Fields
• [Bioperl-guts-l] [Bug 3011] New: namespace support did not work properly for Bio::DB::Seqfeature::Store::DBI::Pg   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3011] namespace support did not work properly for Bio::DB::Seqfeature::Store::DBI::Pg   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16835] bioperl-live/trunk/t/SeqIO/genbank.t: use test_input_file() for file path consistency   Christopher John Fields
• [Bioperl-guts-l] [16836] bioperl-live/trunk/t/Tools/EUtilities/EUtilParameters.t: bioperl -> BioPerl   Christopher John Fields
• [Bioperl-guts-l] [16837] bioperl-live/trunk/t/Root/RootIO.t: TODO failing RootIO test, something borked with HTTPget   Christopher John Fields
• [Bioperl-guts-l] [16838] bioperl-live/trunk: Added support for the '-type' method for specifying what type of sequence object to create in Bio::Seq:: SeqFastaSpeedFactory   Florent E Angly
• [Bioperl-guts-l] [Bug 3012] New: [TODO] Bio::Root::HTTPget tests failing   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3012] [TODO] Bio::Root::HTTPget tests failing   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3012] [TODO] Bio::Root::HTTPget tests failing   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3012] [TODO] Bio::Root::HTTPget tests failing   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3012] [TODO] Bio::Root::HTTPget tests failing   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3012] [TODO] Bio::Root::HTTPget tests failing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16839] bioperl-live/trunk/Bio/Root/IO.pm: fixed #3012   Mark Allen Jensen
  • [Bioperl-guts-l] [16839] bioperl-live/trunk/Bio/Root/IO.pm: fixed #3012   Chris Fields
• [Bioperl-guts-l] [16840] bioperl-live/trunk/t/Root/RootIO.t: no longer a TODO; writing up a couple of simple HTTPget tests for trunk   Christopher John Fields
• [Bioperl-guts-l] [16841] bioperl-live/trunk/t/Root/RootIO.t: add back original URL (wasn' t complete)   Christopher John Fields
• [Bioperl-guts-l] [16842] bioperl-live/trunk: initial tests for HTTPget, including various calls (class, instance, sub)   Christopher John Fields
• [Bioperl-guts-l] [16843] bioperl-live/trunk/t/Assembly/Assembly.t: fix syntax error and test number   Christopher John Fields
• [Bioperl-guts-l] [16844] bioperl-live/trunk/t/Map/Map.t: volatile data fix   Christopher John Fields
• [Bioperl-guts-l] [16845] bioperl-live/trunk: Correcting failures in tests 15 & 36 due to incorrect use of Bio::Species- >species.   Dave Messina
• [Bioperl-guts-l] [16846] bioperl-live/trunk/t/LocalDB/DBFasta.t: get the test count right   Jason Stajich
• [Bioperl-guts-l] [16847] bioperl-live/trunk: rollback Florent's changes that defaulted Bio:: PrimarySeq instead of Bio::Seq creation of objects   Jason Stajich
• [Bioperl-guts-l] [16848] Bio-FeatureIO/trunk: add proper Test suite to local inc as a backup   Christopher John Fields
• [Bioperl-guts-l] [16849] Bio-FeatureIO/trunk: init refactoring of FeatureIO, just a simple stream of Generics at the moment   Christopher John Fields
• [Bioperl-guts-l] [16850] Bio-FeatureIO/trunk/lib/Bio/FeatureIO: add handler   Christopher John Fields
• [Bioperl-guts-l] [16851] Bio-FeatureIO/trunk/lib/Bio/FeatureIO/Handler/GenericHandler.pm: remove redundant handler   Christopher John Fields
• [Bioperl-guts-l] [16852] bioperl-live/trunk/README: test   Christopher John Fields
• [Bioperl-guts-l] bioperl 1.6.1 not on doc.bioperl.org   Dave Messina
  • [Bioperl-guts-l] bioperl 1.6.1 not on doc.bioperl.org   Mauricio Herrera Cuadra
    • [Bioperl-guts-l] bioperl 1.6.1 not on doc.bioperl.org   Dave Messina
• [Bioperl-guts-l] [16853] bioperl-live/trunk/Bio/DB/GFF/Adaptor/dbi.pm: silence warning   Christopher John Fields
• [Bioperl-guts-l] [16854] bioperl-live/trunk/Bio: silence warning (uninit value)   Christopher John Fields
• [Bioperl-guts-l] [16855] bioperl-live/trunk/Bio/SearchIO/blast_pull.pm: rollback accidental blast_pull commit   Christopher John Fields
• [Bioperl-guts-l] [16856] bioperl-live/trunk/t/RemoteDB/Query/GenBank.t: test count changed ( volatile remote data)   Christopher John Fields
• [Bioperl-guts-l] [16857] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: silence warnings about using next w/o a loop   Christopher John Fields
• [Bioperl-guts-l] [16858] bioperl-live/trunk/Bio/SeqIO: defaults to Bio::Seq, so unnecessary   Christopher John Fields
• [Bioperl-guts-l] [16859] bioperl-live/trunk/Bio: really rollback florent's commit, was some cruft hanging around causing fasta to break   Christopher John Fields
• [Bioperl-guts-l] [16860] bioperl-live/trunk/t/SeqIO: really rollback florent's commit, was some cruft hanging around causing fasta to break   Christopher John Fields
• [Bioperl-guts-l] [16861] bioperl-live/trunk/t/SeqIO/metafasta.t: fix bad test file   Christopher John Fields
• [Bioperl-guts-l] [16862] bioperl-live/trunk/Bio/SeqIO/embl.pm: deal with empty buffer warnings   Christopher John Fields
• [Bioperl-guts-l] [16863] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: squash warning   Christopher John Fields
• [Bioperl-guts-l] [16864] bioperl-live/trunk/Bio/LocatableSeq.pm: squash warnings   Christopher John Fields
• [Bioperl-guts-l] [16865] bioperl-live/trunk/Bio/PrimarySeqI.pm: squash warning   Christopher John Fields
• [Bioperl-guts-l] [16866] bioperl-live/trunk/t/LocalDB/DBFasta.t: squish verbose output from tests   Christopher John Fields
• [Bioperl-guts-l] [16867] bioperl-live/trunk: Add id_mapper to SwissProt, and tests   Christopher John Fields
• [Bioperl-guts-l] [16868] bioperl-live/trunk/Bio/DB/SwissProt.pm: add link for database   Christopher John Fields
• [Bioperl-guts-l] [Bug 3014] New: bowtie wrapper, support alternate OS   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3014] bowtie wrapper, support alternate OS   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3014] bowtie wrapper, support alternate OS   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16869] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: bug fix bugzilla #3014   Dan Kortschak
• [Bioperl-guts-l] [16870] bioperl-run/trunk/lib/Bio/Tools/Run/BEDTools.pm: Remove unix command from constructor.   Dan Kortschak
• [Bioperl-guts-l] [16871] bioperl-live/trunk: added noinfer, sofile, manual, conf command line options; added quotemeta to regex strings in OBOEngine. pm; commented out bracket substitution in obo synonym terms for obo.pm; added SO IDs to Typemapper.pm; added noinfer flag to Unflattener.pm   Nathan Liles
• [Bioperl-guts-l] [16872] bioperl-live/trunk/scripts/Bio-DB-GFF/genbank2gff3.PLS: fixed id_validate() to work without needing so.obo file.   Nathan Liles
• [Bioperl-guts-l] [Bug 3015] New: Bug in regex parsing withrefm enzyme cutting site   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3015] Bug in regex parsing withrefm enzyme cutting site   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3015] Bug in regex parsing withrefm enzyme cutting site   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3015] Bug in regex parsing withrefm enzyme cutting site   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2975] Network access despite network tests skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16873] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Follow the bowtie environment variable index location behaviour definition from bowtie manual   Dan Kortschak
• [Bioperl-guts-l] [16874] bioperl-live/trunk/Bio/Restriction/IO/withrefm.pm: bug 3015/ Emmanuel's fixes for negative cut sites   Mark Allen Jensen
• [Bioperl-guts-l] [16875] bioperl-live/trunk/t/Restriction/Analysis-refac.t: added Emmanuel' s tests for bug3015 patch   Mark Allen Jensen
• [Bioperl-guts-l] [16876] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: bugfix provided by Ivica : print bootstrap and branchlength   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [Bug 2975] Network access despite network tests skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16877] bioperl-live/trunk/Bio/PrimarySeq.pm: patched Bio::PrimarySeq. pm to deal with new circular revision genbank spec   Nathan Liles
• [Bioperl-guts-l] [Bug 2975] Network access despite network tests skipped.   bugzilla-daemon at portal.open-bio.org

Last message date: Fri Feb 26 00:13:31 EST 2010
Archived on: Fri Feb 26 00:13:34 EST 2010

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