December 2008 Archives by date

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Starting: Mon Dec 1 03:38:42 EST 2008
Ending: Wed Dec 31 07:14:48 EST 2008
Messages: 358

• [Bioperl-guts-l] [Bug 2691] New: Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15052] bioperl-live/trunk/Bio: make SYNOPSIS code to compile   Heikki Lehvaslaiho
• [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2332] Software for analysis of redundant fragments of affys human mitochip v2   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15053] bioperl-live/trunk/t: reorganising tests by group (1)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15054] bioperl-live/trunk/t/SeqIO/bsml.t: XML::DOM dependancy   Jason Stajich
• [Bioperl-guts-l] [15055] bioperl-live/trunk/t: reorganising tests by group (2: Tree)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [Bug 2695] New: Incorrect processing of ampersand gt/lt entities   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15056] bioperl-live/trunk/t/Tree/TreeIO: reorganising tests by group (2: TreeIO plugins)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15057] bioperl-live/trunk/t: reorganising tests by group (3: Root)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15058] bioperl-live/trunk/t: reorganising tests by group (4: Map)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15059] bioperl-live/trunk/t: reorganising tests by group (4: Map)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15060] bioperl-live/trunk/Bio/HandlerBaseI.pm: small pod fix   Christopher John Fields
• [Bioperl-guts-l] [15061] bioperl-live/trunk/Bio/CodonUsage/Table.pm: Correct typos, runnable Synopsis   Brian Osborne
• [Bioperl-guts-l] [15062] bioperl-live/trunk/t/AlignIO: fix erroneously renamed stockholm tests   Christopher John Fields
• [Bioperl-guts-l] [15063] bioperl-live/trunk/Bio/LocatableSeq.pm: [bug 2450]   Christopher John Fields
• [Bioperl-guts-l] [15064] bioperl-live/trunk/Bio/PrimarySeq.pm: some pod updates   Christopher John Fields
• [Bioperl-guts-l] [15065] bioperl-live/trunk/Bio/Seq/Meta.pm: [bug 2450]   Christopher John Fields
• [Bioperl-guts-l] [15066] bioperl-live/trunk/Bio/SimpleAlign.pm: [bug 2450]   Christopher John Fields
• [Bioperl-guts-l] [15067] bioperl-live/trunk/Bio/AlignIO: [bug 2450]   Christopher John Fields
• [Bioperl-guts-l] [15068] bioperl-live/trunk: [bug 2450]   Christopher John Fields
• [Bioperl-guts-l] [15069] bioperl-live/trunk/t/SearchIO: Add a couple of tests for seq_id ( small but significant inconsistency btwn blast and blast_pull).   Christopher John Fields
• [Bioperl-guts-l] [15070] bioperl-live/trunk/t/SearchIO/blast_pull.t: forgot to increment test count   Christopher John Fields
• [Bioperl-guts-l] [15071] bioperl-live/trunk/t: small updates:   Christopher John Fields
• [Bioperl-guts-l] [15072] bioperl-live/trunk/t: Start Tools move   Christopher John Fields
• [Bioperl-guts-l] [15073] bioperl-live/trunk/t: Remove old files   Christopher John Fields
• [Bioperl-guts-l] [15074] bioperl-live/trunk: Add method that finds the most common codons for the aa's, uses those to reverse-translate a nucleotide sequence   Brian Osborne
• [Bioperl-guts-l] [15075] bioperl-live/trunk/t/PhylipDist.t: Remove redundant file   Christopher John Fields
• [Bioperl-guts-l] [15076] bioperl-live/trunk/t: Merge tests   Christopher John Fields
• [Bioperl-guts-l] [15077] bioperl-live/trunk/t/Tools/SeqWords.t: Update test count   Christopher John Fields
• [Bioperl-guts-l] [15078] bioperl-live/trunk/t: Merge tests and remove redundant file   Christopher John Fields
• [Bioperl-guts-l] [15079] bioperl-live/trunk/t/trim.t: Remove (tests are redundant, in Consed .t)   Christopher John Fields
• [Bioperl-guts-l] [15080] bioperl-live/trunk/t: Reorganize Tools tests ( needs some more splitting)   Christopher John Fields
• [Bioperl-guts-l] [15081] bioperl-live/trunk/t: Remove files accidently added from last commit   Christopher John Fields
• [Bioperl-guts-l] [15082] bioperl-live/trunk/Bio/Tools/SeqStats.pm: Clarify what frame is used by count_codons   Brian Osborne
• [Bioperl-guts-l] [Bug 2696] New: global verbosity does not propagate to new objects post-set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2696] global verbosity does not propagate to new objects post-set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2696] global verbosity does not propagate to new objects post-set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15083] bioperl-live/trunk/t: reorganising tests by group (5: rest)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15084] bioperl-live/trunk: leave ID undefined if it isn't present, but allow the NSE to be created if forced ( this may need revisiting in the future)   Christopher John Fields
• [Bioperl-guts-l] [15085] bioperl-live/trunk/t/Seq/LocatableSeq.t: add force_nse tests   Christopher John Fields
• [Bioperl-guts-l] [15086] bioperl-live/trunk: fixed default of ##index-subfeatures to true so that it behaves the way that it is documented to work   Lincoln Stein
• [Bioperl-guts-l] [15087] bioperl-live/trunk/examples: Add script that demonstrates reverse_tranlate_best()   Brian Osborne
• [Bioperl-guts-l] [15088] bioperl-live/trunk/scripts: svn propset Id   Brian Osborne
• [Bioperl-guts-l] [15089] bioperl-live/trunk/t/DB/: Directory is no longer needed ( Heikki split this up into LocalDB and RemoteDB)   Christopher John Fields
• [Bioperl-guts-l] [15090] bioperl-live/trunk: remove t/sequencetrace. t and add missing method tests into t/SeqIO/scf ( could be split into IO and storage class spesific tests)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15091] bioperl-live/trunk/Bio/SeqFeature/Generic.pm: interpro XML parser tries to assign "NA" into a numeric "score" field.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [Bug 2696] global verbosity does not propagate to new objects post-set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2696] global verbosity does not propagate to new objects post-set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15092] bioperl-live/trunk/Bio/Annotation/Target.pm: Make Target a true DBLink   Christopher John Fields
• [Bioperl-guts-l] [15093] bioperl-live/trunk: [bug 2450]   Christopher John Fields
• [Bioperl-guts-l] [15094] bioperl-live/trunk/t/Tree/TreeIO/svggraph.t: Need to retrieve the tree for output   Christopher John Fields
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2463] bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2594] Bio::Species memory leak   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15095] bioperl-live/trunk: improved message for genemap read error to suggest possible solution; also added test for catching this error.   Dave Messina
• [Bioperl-guts-l] [15096] bioperl-live/trunk/t/Phenotype/OMIMparser.t: forgot a linebreak.   Dave Messina
• [Bioperl-guts-l] [15097] bioperl-live/trunk/Bio/PopGen/Utilities.pm: demonstrate with a valid 'site_model' as 'codons' rather than unimplemented 'syn'   Jason Stajich
• [Bioperl-guts-l] [15098] bioperl-network/trunk: bioperl-network now requires Graph v.   Brian Osborne
• [Bioperl-guts-l] [15099] bioperl-network/trunk: bioperl-network now requires Graph v.   Brian Osborne
• [Bioperl-guts-l] [15100] bioperl-network/trunk/README: bioperl-network now requires Graph v.   Brian Osborne
• [Bioperl-guts-l] [15101] bioperl-network/trunk/Bio/Network/ProteinNet.pm: bioperl-network now requires Graph v.   Brian Osborne
• [Bioperl-guts-l] [15102] bioperl-network/trunk/Bio/Network/ProteinNet.pm: bioperl-network now requires Graph v.   Brian Osborne
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2699] New: BioDBGFF.t setup in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2699] BioDBGFF.t setup in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15103] bioperl-live/trunk/Build.PL: [bug 2699]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2699] BioDBGFF.t setup in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2700] New: [TODO] Refactor Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2700] [TODO] Refactor Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New: New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2700] [TODO] Refactor Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2700] [TODO] Refactor Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2700] [TODO] Refactor Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2702] New: [TODO] scripts recopied upon each call to './Build test'   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2703] New: Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2703] Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2703] Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15104] bioperl-live/trunk/Bio/AlignIO/meme.pm: evalue now parsed and set as score   Senduran Balasubramaniam
• [Bioperl-guts-l] [15105] bioperl-network/trunk: ModuleBuildBioperl -> Bio::Root::Build   Senduran Balasubramaniam
• [Bioperl-guts-l] [15106] bioperl-db/trunk: ModuleBuildBioperl -> Bio::Root::Build   Senduran Balasubramaniam
• [Bioperl-guts-l] [15107] bioperl-run/trunk: ModuleBuildBioperl -> Bio::Root::Build   Senduran Balasubramaniam
• [Bioperl-guts-l] [15108] bioperl-run/trunk/t: BioperlTest -> Bio::Root::Test   Senduran Balasubramaniam
• [Bioperl-guts-l] [15109] bioperl-live/trunk: ModuleBuildBioperl -> Bio::Root::Build   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2703] Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15110] bioperl-live/trunk/Bio/Map: new ability to define what is consered an overlap   Senduran Balasubramaniam
• [Bioperl-guts-l] [15111] bioperl-live/trunk/Bio/DB/SeqFeature: gain-of-function changes for mysql implementation only: features are searchable by source, and you can avoid freezing objects to the db for size and speed benefits; was unable to get any feedback from the maintainer about this change - maintainer may revert if this is undesireable   Senduran Balasubramaniam
• [Bioperl-guts-l] [15112] bioperl-live/trunk: BioperlTest -> Bio::Root::Test   Senduran Balasubramaniam
• [Bioperl-guts-l] [15113] bioperl-live/trunk/AUTHORS: Updated emails   Christopher John Fields
• [Bioperl-guts-l] [15114] bioperl-live/trunk/AUTHORS: Roy's email (and bioperl. org not bioperl.edu)   Christopher John Fields
• [Bioperl-guts-l] [15115] bioperl-live/trunk/Bio/SeqUtils.pm: Update Roy's email   Christopher John Fields
• [Bioperl-guts-l] [15116] bioperl-live/trunk/AUTHORS: I'm a core dev   Brian Osborne
• [Bioperl-guts-l] [Bug 2686] WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2686] WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15117] bioperl-live/trunk/AUTHORS: adding myself to author list   Dave Messina
• [Bioperl-guts-l] [15118] bioperl-live/trunk/AUTHORS: added my info   Scott Cain
• [Bioperl-guts-l] [15119] bioperl-live/trunk: Bio::Graphics has become its own module; latest version is uploaded to CPAN   Lincoln Stein
• [Bioperl-guts-l] [15120] bioperl-live/trunk: update Mauricio's email   Christopher John Fields
• [Bioperl-guts-l] [15121] bioperl-live/trunk/t/Root/RootI.t: Modify to test new temp classes and ensure that added methods do not pollute original namespace   Christopher John Fields
• [Bioperl-guts-l] [15122] bioperl-live/trunk/t/Root/RootI.t: Fix last loop tests, move some to can_ok   Christopher John Fields
• [Bioperl-guts-l] [Bug 2332] Software for analysis of redundant fragments of affys human mitochip v2   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15123] bioperl-live/trunk/t/Tree/TreeIO/phyloxml.t: diag() only on verbose   Christopher John Fields
• [Bioperl-guts-l] [15124] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: Squash warning   Christopher John Fields
• [Bioperl-guts-l] [15125] bioperl-live/trunk/Bio/Graphics.pm: removed Bio::Graphics itself   Lincoln Stein
• [Bioperl-guts-l] [15126] bioperl-live/trunk/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: fixed issue of score and phase fields disappearing from the first part of a multi-child feature   Lincoln Stein
• [Bioperl-guts-l] [15127] bioperl-live/trunk/Build.PL: Remove dependencies for Bio:: Graphics and deprecated modules   Christopher John Fields
• [Bioperl-guts-l] [15128] bioperl-live/trunk/AUTHORS: [bug 2637]   Christopher John Fields
• [Bioperl-guts-l] [15129] bioperl-live/trunk/Build.PL: remove Bio::Graphics ( separate package now)   Christopher John Fields
• [Bioperl-guts-l] [15130] bioperl-live/trunk/DEPRECATED: update deprecation list   Christopher John Fields
• [Bioperl-guts-l] [Bug 2699] BioDBGFF.t setup in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2706] New: bioperl-live install issue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2706] bioperl-live install issue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2706] bioperl-live install issue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15131] bioperl-live/trunk/Bio/Microarray/Tools: Bug Fixes, New Feature: different Fasta Files (e.g.   Marian Thieme
• [Bioperl-guts-l] [15132] bioperl-live/trunk/t: Providing Testscript for ReseqChip   Marian Thieme
• [Bioperl-guts-l] [15133] bioperl-live/trunk/t/data: Test/Example Data for ReseqChip   Marian Thieme
• [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide   Marian Thieme
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2707] New: Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in filenames, but Bio::SearchIO::blast does   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2707] Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in filenames, but Bio::SearchIO::blast does   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2706] bioperl-live install issue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15135] bioperl-live/trunk/Bio/Taxon.pm: mini pod fix   Christopher John Fields
• [Bioperl-guts-l] [15136] bioperl-live/trunk/Bio: Removing from HEAD (deprecated for 1.6)   Christopher John Fields
• [Bioperl-guts-l] [15137] bioperl-live/trunk/Bio/DB/SeqFeature: added simple feature deletion script   Lincoln Stein
• [Bioperl-guts-l] [15138] bioperl-live/trunk/scripts/Bio-SeqFeature-Store/ bp_seqfeature_delete.PLS: added simple feature deletion script, take 2   Lincoln Stein
• [Bioperl-guts-l] [15139] bioperl-live/trunk/Bio/Tools/Run: [bug 2707]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2707] Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in filenames, but Bio::SearchIO::blast does   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15140] bioperl-live/trunk/Build.PL: [bug 2699]   Christopher John Fields
• [Bioperl-guts-l] [15141] bioperl-live/trunk/t/LocalDB/BioDBGFF.t: [bug 2699]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2699] BioDBGFF.t setup in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2695] Incorrect processing of ampersand gt/lt entities   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2708] New: Bio::Assembly::Contig->get_seq_by_name dies when it should return undef   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2708] Bio::Assembly::Contig->get_seq_by_name dies when it should return undef   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2708] Bio::Assembly::Contig->get_seq_by_name dies when it should return undef   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15142] bioperl-live/trunk/Bio: return, not 'return undef'   Christopher John Fields
• [Bioperl-guts-l] [15143] bioperl-live/trunk/Bio/SimpleAlign.pm: return, not 'return undef'   Christopher John Fields
• [Bioperl-guts-l] [15144] bioperl-live/trunk/README: updates   Christopher John Fields
• [Bioperl-guts-l] [15145] bioperl-live/trunk/PLATFORMS: small update   Christopher John Fields
• [Bioperl-guts-l] [15146] bioperl-live/trunk/INSTALL: small pointer to wiki page ( will update along with wiki closer to release)   Christopher John Fields
• [Bioperl-guts-l] [15147] bioperl-live/trunk/Bio/DB/GenericWebAgent.pm: fix for bug when getting cached response with filename or callback ( prevents resubing the request)   Christopher John Fields
• [Bioperl-guts-l] [15148] bioperl-live/trunk: Adding the postgres adaptor for SeqFeature:: Store; doesn't pass tests yet!   Scott Cain
• [Bioperl-guts-l] [Bug 2699] BioDBGFF.t setup in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15149] bioperl-live/trunk/Bio: Do not use "return undef" unless you really know that it is necessary.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15150] bioperl-live/trunk: new parser for the Match program from transfac   Senduran Balasubramaniam
• [Bioperl-guts-l] [15151] bioperl-live/trunk/Bio: Move EUtilParameters to Tools ( seems more appropriate)   Christopher John Fields
• [Bioperl-guts-l] [15152] bioperl-live/trunk/Bio: updates to EUtilities ( getting ready for docs, tests, etc)   Christopher John Fields
• [Bioperl-guts-l] [15153] bioperl-live/trunk/t/data: some test data for Bio::Tools:: EUtilities   Christopher John Fields
• [Bioperl-guts-l] [15154] bioperl-live/trunk/t/Tools: some EUtilities tests ( parsing from files)   Christopher John Fields
• [Bioperl-guts-l] [15155] bioperl-live/trunk/t/Tools/EUtilities/einfo.t: einfo tests   Christopher John Fields
• [Bioperl-guts-l] [15156] bioperl-live/trunk/t/Tools/EUtilities/EUtilParameters.t: initial batch of EUtilParameters tests   Christopher John Fields
• [Bioperl-guts-l] [Bug 2498] Add HSP sorting to Bio::Search::Hit   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15157] bioperl-live/trunk/t/data/dcr1_sp.WUBLASTP: another example BLAST   Jason Stajich
• [Bioperl-guts-l] [Bug 2498] Add HSP sorting to Bio::Search::Hit   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15158] bioperl-live/trunk/Build.PL: minor comment correntions   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2712] New: Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2712] Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2712] Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2712] Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2712] Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15159] bioperl-live/trunk: Bio:: Map extended to model transcription factors and their binding sites   Senduran Balasubramaniam
• [Bioperl-guts-l] [15160] bioperl-live/trunk/Bio: Updates:   Christopher John Fields
• [Bioperl-guts-l] [15161] bioperl-live/trunk/t/data/eutils: more test data   Christopher John Fields
• [Bioperl-guts-l] [15162] bioperl-live/trunk/t/Tools/EUtilities: remaining tests for Bio:: Tool::EUtilities   Christopher John Fields
• [Bioperl-guts-l] [Bug 2712] Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15163] bioperl-live/trunk/Bio/Tools/EUtilities/Link/LinkSet.pm: scores   Christopher John Fields
• [Bioperl-guts-l] [15164] bioperl-live/trunk/Bio/SearchIO/fasta.pm: [bug 2712]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2712] Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15165] bioperl-live/trunk/Bio/DB: [bug 2637]   Christopher John Fields
• [Bioperl-guts-l] [15166] bioperl-live/trunk/Bio/DB: [bug 2637]   Christopher John Fields
• [Bioperl-guts-l] [15167] bioperl-live/trunk/Bio/DB/HIV.pm: [bug 2637]   Christopher John Fields
• [Bioperl-guts-l] [15168] bioperl-live/trunk/t/RemoteDB: [bug 2637]   Christopher John Fields
• [Bioperl-guts-l] [15169] bioperl-live/trunk/Build.PL: [bug 2637]   Christopher John Fields
• [Bioperl-guts-l] [15170] bioperl-live/trunk/Bio/Tree/Node.pm: hash ref, not array ref   Christopher John Fields
• [Bioperl-guts-l] [15171] bioperl-live/trunk/Bio/Root/Exception.pm: stifle warnings when passing string instead of integer   Christopher John Fields
• [Bioperl-guts-l] [15172] bioperl-live/trunk/t/protgraph.t: Bio::Graph deprecated in 1.6   Christopher John Fields
• [Bioperl-guts-l] [15173] bioperl-live/trunk/t/Annotation/Annotation.t: indentation and formatting only   Jason Stajich
• [Bioperl-guts-l] [15174] bioperl-live/trunk/Bio/Microarray/Tools: Don' t use print! Changing to $self->debug or commenting out   Christopher John Fields
• [Bioperl-guts-l] [15175] bioperl-live/trunk/t/Microarray/Tools/ReseqChip.t: You must actually test data if you want this module to be included in the release (this now fails two tests)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2594] Bio::Species memory leak   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2332] Software for analysis of redundant fragments of affys human mitochip v2   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2345] Get mappable sequence coords after removing alignment columns   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2713] New: [TODO] Update core Infernal parsing to v1.0, add related tests to bioperl-run   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15176] bioperl-live/trunk: parse DBlinks now supported   Jason Stajich
• [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2695] Incorrect processing of ampersand gt/lt entities   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15177] bioperl-live/trunk/t/Tree/TreeIO/svggraph.t: skip test count updated for instances when SVG::Graph is not installed   Jason Stajich
• [Bioperl-guts-l] [Bug 2712] Error reading fastx35 output with bioperl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15178] bioperl-live/trunk: new test method test_output_dir(), a wrapper around Temp::File::tempdir   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15179] bioperl-live/trunk: new transfac pro database parser   Senduran Balasubramaniam
• [Bioperl-guts-l] [15180] bioperl-live/trunk/Bio/DB/TFBS/transfac_pro.pm: added POD docs   Senduran Balasubramaniam
• [Bioperl-guts-l] [15181] bioperl-run/trunk/t/lib/BioperlTest.pm: t/lib/BioperlTest.pm -> Bio ::Root::Test   Senduran Balasubramaniam
• [Bioperl-guts-l] [15182] bioperl-run/trunk/t/tRNAscanSE.t: t/lib/BioperlTest.pm -> Bio::Root ::Test   Senduran Balasubramaniam
• [Bioperl-guts-l] [15183] bioperl-run/trunk/t/Gerp.t: make even more sure extracted file gets deleted   Senduran Balasubramaniam
• [Bioperl-guts-l] [15184] bioperl-run/trunk/Bio/Tools/Run/Meme.pm: new MEME parser, docs and tests to follow   Senduran Balasubramaniam
• [Bioperl-guts-l] [15185] bioperl-run/trunk/Bio/Tools/Run/Match.pm: new Match parser, tests to follow   Senduran Balasubramaniam
• [Bioperl-guts-l] [15186] bioperl-run/trunk/Bio/Tools/Run/Ensembl.pm: new wrapper around Ensembe, improved docs and tests to follow   Senduran Balasubramaniam
• [Bioperl-guts-l] [15187] bioperl-run/trunk/Bio/Tools/Run/Phylo/Semphy.pm: new Semphy wrapper , tests to follow   Senduran Balasubramaniam
• [Bioperl-guts-l] [15188] bioperl-run/trunk/Bio/Tools/Run/Alignment/Pal2Nal.pm: new Pal2Nal wrapper, tests to follow   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15189] bioperl-live/trunk/t/RemoteDB/EUtilities.t: EUtilities remote tests back online (simple tests only)   Christopher John Fields
• [Bioperl-guts-l] [15190] bioperl-live/trunk/t/RemoteDB/EUtilities/: EUtilities remote tests back online (simple tests only)   Christopher John Fields
• [Bioperl-guts-l] [15191] bioperl-live/trunk/Bio/Tools/EUtilities/Summary/DocSum.pm: missed one   Christopher John Fields
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15192] bioperl-live/trunk/Bio/DB/TFBS/transfac_pro.pm: passing $1 is bad in perl 5.10? - fixed   Senduran Balasubramaniam
• [Bioperl-guts-l] [15193] bioperl-live/trunk/t/LocalDB/transfac_pro.t: no longer assumes added order of ids in tests   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15194] bioperl-live/trunk/t/lib/Test/Warn.pm: update Test::Warn ( fixes Qual.t test problems with warnings_like)   Christopher John Fields
• [Bioperl-guts-l] [15195] bioperl-live/trunk/t/Seq/Quality.t: fix test number   Christopher John Fields
• [Bioperl-guts-l] [15196] bioperl-run/trunk/Bio/Tools/Run: fixed copy-pasted obtiained typo in POD   Senduran Balasubramaniam
• [Bioperl-guts-l] [15197] bioperl-run/trunk/t: use test_input_dir(), Bio::Root::Test   Senduran Balasubramaniam
• [Bioperl-guts-l] [15198] bioperl-run/trunk/Bio/Tools/Run/Phylo/Semphy.pm: minor comment correction   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15199] bioperl-run/trunk/Bio/Tools/Run/Meme.pm: reimplemented to modern style, added POD   Senduran Balasubramaniam
• [Bioperl-guts-l] [15200] bioperl-run/trunk/t/Meme.t: test script for Meme wrapper   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15201] bioperl-run/trunk/Bio/Tools/Run/Ensembl.pm: added POD   Senduran Balasubramaniam
• [Bioperl-guts-l] [15202] bioperl-run/trunk/t/Ensembl.t: test script for the Ensembl wrapper   Senduran Balasubramaniam
• [Bioperl-guts-l] [15203] bioperl-run/trunk/Bio/Tools/Run/Match.pm: corrected ENV setting, fixed file location bug   Senduran Balasubramaniam
• [Bioperl-guts-l] [15204] bioperl-run/trunk/t: test script and data for match wrapper   Senduran Balasubramaniam
• [Bioperl-guts-l] [15205] bioperl-run/trunk/t: test script and data for Pal2Nal wrapper   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2714] New: key HIVQuery patches   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2714] key HIVQuery patches   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2714] key HIVQuery patches   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2714] key HIVQuery patches   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2714] key HIVQuery patches   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2715] New: [TODO] LocatableSeq symbols are globally set (should be localized)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2714] key HIVQuery patches   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15206] bioperl-live/trunk: [bug 2714]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2714] key HIVQuery patches   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15207] bioperl-live/trunk/t/Seq/LocatableSeq.t: typo   Christopher John Fields
• [Bioperl-guts-l] [Bug 2715] [TODO] LocatableSeq symbols are globally set (should be localized)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15208] bioperl-live/trunk/t/RemoteDB/HIV/HIV.t: skip right number of tests needing the network   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15209] bioperl-run/trunk/Bio/Tools/Run/Phylo/Semphy.pm: added new params and switches for semphy 2   Senduran Balasubramaniam
• [Bioperl-guts-l] [15210] bioperl-run/trunk/t: test script and data for semphy wrapper   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2715] [TODO] LocatableSeq symbols are globally set (should be localized)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15211] bioperl-live/trunk/Bio/Biblio.pm: small typo   Christopher John Fields
• [Bioperl-guts-l] [15212] bioperl-live/trunk/Bio: update NAMES   Christopher John Fields
• [Bioperl-guts-l] [15213] bioperl-live/trunk/Bio/FeatureIO: 5.6. 1 is min perl version required for all core modules now   Christopher John Fields
• [Bioperl-guts-l] [15214] bioperl-live/branches/branch-1-6/: Created branch branch-1-6.   Christopher John Fields
• [Bioperl-guts-l] [Bug 2696] global verbosity does not propagate to new objects post-set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15215] bioperl-live/trunk/Bio/Tools/BPlite/: Removed in 1.6.   Christopher John Fields
• [Bioperl-guts-l] [15216] bioperl-live/trunk/Bio: Remove BPlite from use   Christopher John Fields
• [Bioperl-guts-l] [15217] bioperl-live/trunk/Bio/Search/Result: Update docs   Christopher John Fields
• [Bioperl-guts-l] [15218] bioperl-live/trunk/Bio/Search/Result/BlastResult.pm: Update docs   Christopher John Fields
• [Bioperl-guts-l] [15219] bioperl-live/trunk/examples/tk/hitdisplay.pl: add deprecation message and indicate that this example needs refactoring to work with more modern code in trunk   Christopher John Fields
• [Bioperl-guts-l] [15220] bioperl-live/trunk/t/Tools/Run/StandAloneBlast.t: remove BPlite tests completely   Christopher John Fields
• [Bioperl-guts-l] [15221] bioperl-live/trunk/DEPRECATED: we're keeping Bio::Root:: Utilities per Steve C (I think)   Christopher John Fields
• [Bioperl-guts-l] [15222] bioperl-live/trunk/Bio/Tools: add deprecation messagess   Christopher John Fields
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Christopher John Fields
• [Bioperl-guts-l] [15224] bioperl-live/trunk/Bio/SeqFeature/Annotated.pm: small typo   Christopher John Fields
• [Bioperl-guts-l] [15225] bioperl-live/trunk/Build.PL: For Marian's Bio::Microarray modules   Christopher John Fields
• [Bioperl-guts-l] [15226] bioperl-live/trunk/Bio/DB/NCBIHelper.pm: no VERSION   Christopher John Fields
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Sendu Bala
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Chris Fields
• [Bioperl-guts-l] [15227] bioperl-live/trunk/maintenance/deprecated.pl: Add maintenance script to check modules for possible deprecated module use , generate new DEPRECATED file with simple input.   Christopher John Fields
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Sendu Bala
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Chris Fields
• [Bioperl-guts-l] [Bug 2717] New: Problem regarding installing -ext package   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Sendu Bala
• [Bioperl-guts-l] [Bug 2717] Problem regarding installing -ext package   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Chris Fields
• [Bioperl-guts-l] [15228] bioperl-live/trunk/Bio/Root: * Downgrade VERSION to 1.5. 9_001 per dev list discussion, quote for extended versioning ( which we already have anyway).   Christopher John Fields
• [Bioperl-guts-l] [Bug 2492] Method "pi" in package Bio::PopGen::Statistics   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15229] bioperl-live/trunk/Bio/Tools/Phylo/PAML.pm: [bug 2690]   Christopher John Fields
• [Bioperl-guts-l] [15230] bioperl-live/trunk/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: extended FeatureFile loader to allow for named subtypes of features; also fixed documentation   Lincoln Stein
• [Bioperl-guts-l] [15231] bioperl-live/branches/branch-1-6: sync trunk with branch   Christopher John Fields
• [Bioperl-guts-l] [15232] bioperl-live/trunk/INSTALL: update INSTALL   Christopher John Fields
• [Bioperl-guts-l] [15231] bioperl-live/branches/branch-1-6: sync trunk with branch   Chris Fields
• [Bioperl-guts-l] [15233] bioperl-live/trunk/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: fixed inadvertent loss of strandedness when converting a one-level feature into a multi-level feature   Lincoln Stein
• [Bioperl-guts-l] [15234] bioperl-live/trunk/Bio/SeqIO/agave.pm: remove user-dependent local lib directives   Christopher John Fields
• [Bioperl-guts-l] [15235] bioperl-live/trunk/Bio/Ontology/SimpleGOEngine: * Add back the GraphAdaptor modules (many many Ontology test break w/ o these, errors are masked by old bioperl installations)   Christopher John Fields
• [Bioperl-guts-l] [15236] bioperl-live/trunk/Bio/DB/Query/HIVQuery.pm: word wrap   Christopher John Fields
• [Bioperl-guts-l] [15237] bioperl-live/trunk/Bio/DB/HIV/HIVQueryHelper.pm: Namespaces are important   Christopher John Fields
• [Bioperl-guts-l] [15238] bioperl-live/trunk/Bio: minor fixes   Christopher John Fields
• [Bioperl-guts-l] [15239] bioperl-live/trunk/Bio/Tools/Lucy.pm: use Root::warn or debug, not print   Christopher John Fields
• [Bioperl-guts-l] [15240] bioperl-live/trunk/Bio: * Min required version for core 1.6 is 5.6. 1   Christopher John Fields
• [Bioperl-guts-l] [15241] bioperl-live/trunk/Bio/Graph/: Delete unused Graph directory ( deprecated in favor of bioperl-network)   Christopher John Fields
• [Bioperl-guts-l] [15242] bioperl-live/trunk: * Add script to autogenerate DEPENDENCIES file (as DEPENDENCIES.NEW)   Christopher John Fields
• [Bioperl-guts-l] [15243] bioperl-live/trunk/Bio/LiveSeq/IO/Loader.pm: small change ( helps with script)   Christopher John Fields
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15244] bioperl-live/trunk/maintenance/dependencies.pl: minor grammar fix   Senduran Balasubramaniam
• [Bioperl-guts-l] [15245] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm: dropped usage of external Bio::Graphics::Feature for core's new Bio:: SeqFeature::Lite   Senduran Balasubramaniam
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Hilmar Lapp
• [Bioperl-guts-l] [15246] bioperl-live/trunk: * update script docs, clean, use only unique names   Christopher John Fields
• [Bioperl-guts-l] [15247] bioperl-live/trunk/maintenance/dependencies.pl: shouldn' t need perl 5.10   Christopher John Fields
• [Bioperl-guts-l] [15223] bioperl-live/trunk/Bio/Root: Bump VERSION to 1.6 RC1 (or 1. 006000_001)   Chris Fields
• [Bioperl-guts-l] [15246] bioperl-live/trunk: * update script docs, clean, use only unique names   Sendu Bala
• [Bioperl-guts-l] [15248] bioperl-live/trunk/DEPENDENCIES: * forgot to update ( thanks to Sendu fo pointing this out)   Christopher John Fields
• [Bioperl-guts-l] [15249] bioperl-live/trunk/examples/biographics/: * remove from core (Bio:: Graphics has left the building)   Christopher John Fields
• [Bioperl-guts-l] [15250] bioperl-live/trunk/scripts/biographics/: * remove from core (Bio:: Graphics has left the building)   Christopher John Fields
• [Bioperl-guts-l] [15246] bioperl-live/trunk: * update script docs, clean, use only unique names   Chris Fields
• [Bioperl-guts-l] [15251] bioperl-live/trunk/t/Tools/rnamotif.t: modules are deprecated   Christopher John Fields
• [Bioperl-guts-l] [15252] bioperl-live/trunk: * set timeouts for UA ( HIVQuery needs a way to set this using a method, ie.   Christopher John Fields
• [Bioperl-guts-l] [15253] bioperl-live/trunk/maintenance/dependencies.pl: small svn tag fix   Christopher John Fields
• [Bioperl-guts-l] [15254] bioperl-live/branches/branch-1-6/Bio/Tools/BPlite: Remove ( merge didn't remove this for some reason)   Christopher John Fields
• [Bioperl-guts-l] [15255] bioperl-live/branches/branch-1-6/Bio/Graph/: Remove (merge didn' t remove this for some reason)   Christopher John Fields
• [Bioperl-guts-l] [15256] bioperl-live/branches/branch-1-6: Remove Bio:: Microarray from branch (still in development on trunk).   Christopher John Fields
• [Bioperl-guts-l] [15257] bioperl-live/branches/branch-1-6: Sync branch with trunk   Christopher John Fields
• [Bioperl-guts-l] [15258] bioperl-live/branches/branch-1-6/t/RemoteDB/HIV/HIVQuery.t: Small fix for tests JIC there is a network error   Christopher John Fields
• [Bioperl-guts-l] [15259] bioperl-live/trunk: merge back some changes from the branch   Christopher John Fields
• [Bioperl-guts-l] [15260] bioperl-live/branches/branch-1-6/Build.PL: remove Microarray deps   Christopher John Fields
• [Bioperl-guts-l] [15261] bioperl-live/branches/branch-1-6: Updates for RC1   Christopher John Fields
• [Bioperl-guts-l] [15262] bioperl-live/branches/branch-1-6/BUGS: Add list of bugs slated for the 1.6.x series   Christopher John Fields
• [Bioperl-guts-l] [15263] bioperl-live/branches/branch-1-6/BUGS: small clarification   Christopher John Fields
• [Bioperl-guts-l] [15264] bioperl-live/trunk: * merge back from the 1.6 branch   Christopher John Fields
• [Bioperl-guts-l] [15265] bioperl-live/trunk/Bio/Root: Trunk is now designated 1.007   Christopher John Fields
• [Bioperl-guts-l] [15266] bioperl-live/tags/bioperl-1-6-RC1/: Tagging RC1   Christopher John Fields
• [Bioperl-guts-l] [15267] bioperl-live/trunk/t/SeqIO/strider.t: require Convert::Binary::C ( tests failing with 1.6 RC1, CPAN Testers)   Christopher John Fields
• [Bioperl-guts-l] [15268] bioperl-live/branches/branch-1-6/t/SeqIO/strider.t: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15269] bioperl-live/branches/branch-1-6/Bio/Microarray/: empty directory   Christopher John Fields
• [Bioperl-guts-l] [15270] bioperl-live/branches/branch-1-6/Bio/Tools/BPlite/: Empty directory   Christopher John Fields
• [Bioperl-guts-l] [15271] bioperl-live/branches/branch-1-6/t/Microarray/: empty directory   Christopher John Fields
• [Bioperl-guts-l] [Bug 2719] New: HIVQuery can't find its XML   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2719] HIVQuery can't find its XML   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2720] New: additional HIVQuery annotation access functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2720] additional HIVQuery annotation access functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2720] additional HIVQuery annotation access functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2719] HIVQuery can't find its XML; Incremental query run is broken   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2719] HIVQuery can't find its XML; Incremental query run is broken   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15272] bioperl-live/trunk/Build.PL: the distribution name is BioPerl, not bioperl   Senduran Balasubramaniam
• [Bioperl-guts-l] [15273] bioperl-run/trunk/Build.PL: the distribution name is BioPerl, not bioperl; version bump for trunc   Senduran Balasubramaniam
• [Bioperl-guts-l] [15274] bioperl-db/trunk/Build.PL: the distribution name is BioPerl, not bioperl; version bump for trunc   Senduran Balasubramaniam
• [Bioperl-guts-l] [15275] bioperl-run/trunk/Build.PL: the distribution name is BioPerl, not bioperl; version bump for trunc, try2   Senduran Balasubramaniam
• [Bioperl-guts-l] [15276] bioperl-db/trunk/Build.PL: the distribution name is BioPerl, try2   Senduran Balasubramaniam
• [Bioperl-guts-l] [15277] bioperl-network/trunk/Build.PL: the distribution name is BioPerl, not bioperl; version bump for trunc   Senduran Balasubramaniam
• [Bioperl-guts-l] [15278] bioperl-live/trunk/Build.PL: the distribution name is BioPerl, try2   Senduran Balasubramaniam

Last message date: Wed Dec 31 07:14:48 EST 2008
Archived on: Wed Dec 31 07:14:53 EST 2008

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