January 2009 Archives by thread

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Starting: Thu Jan 1 20:30:03 EST 2009
Ending: Sat Jan 31 23:53:22 EST 2009
Messages: 307

• [Bioperl-guts-l] [Bug 2074] bioperl-ext: make test fails using io_lib v. 1.9 or higher   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 2721] New: improve documentation of mrtrans.pl   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2721] improve documentation of mrtrans.pl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15279] bioperl-live/branches/branch-1-6: Remove Bio:: Graphics examples and scripts   Christopher John Fields
• [Bioperl-guts-l] [15280] bioperl-live/branches/branch-1-6/t/Graphics/: Remove t/Graphics   Christopher John Fields
• [Bioperl-guts-l] [15281] bioperl-live/trunk/t/Graphics/: Remove t/Graphics from trunk   Christopher John Fields
• [Bioperl-guts-l] [15282] bioperl-live/trunk/t: required modules via CPAN Tester failed tests   Christopher John Fields
• [Bioperl-guts-l] [15283] bioperl-live/branches/branch-1-6/t: sync with HEAD   Christopher John Fields
• [Bioperl-guts-l] [15284] bioperl-live/trunk/t/Tools/EUtilities/egquery.t: left off comma   Christopher John Fields
• [Bioperl-guts-l] [15285] bioperl-live/branches/branch-1-6/t/Tools/EUtilities/egquery.t: sync last commit   Christopher John Fields
• [Bioperl-guts-l] [15286] bioperl-live/trunk/Bio/Tools/Phylo/PAML.pm: Possible fix for CPAN testers failed PAML test, Linux, perl 5.8.7   Christopher John Fields
• [Bioperl-guts-l] [15287] bioperl-live/branches/branch-1-6/Bio/Tools/Phylo/PAML.pm: sync from trunk   Christopher John Fields
• [Bioperl-guts-l] [Bug 2722] New: HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2722] HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2722] HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2722] HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2722] HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2722] HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2722] HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2722] HIVQuery table joins are incompletely specified   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15288] bioperl-live/trunk/Bio/DB: [bug 2719, 2720, 2722]   Christopher John Fields
• [Bioperl-guts-l] [15289] bioperl-live/branches/branch-1-6/Bio/DB: sync with trunk   Christopher John Fields
• [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 2720] additional HIVQuery annotation access functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15290] bioperl-live/trunk/t/RemoteDB: Skip correct number of tests   Christopher John Fields
• [Bioperl-guts-l] [15291] bioperl-live/branches/branch-1-6/t/RemoteDB: Sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15292] bioperl-live/branches/branch-1-6/Bio/Root: Bump RC to 2; will tag, bag, and ship tomorrow after tests   Christopher John Fields
• [Bioperl-guts-l] [15293] bioperl-experimental/trunk/:   Christopher John Fields
• [Bioperl-guts-l] [15294] bioperl-live/trunk: Add back Shawn Hoon' s Pictogram module and tests, but rename to Bio::Draw::Pictogram ( per Lincoln).   Christopher John Fields
• [Bioperl-guts-l] [15295] bioperl-live/trunk: update DEPENDENCIES and Build.PL for SVG (Bio:: Draw::Pictogram)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2725] New: New modules for alignment graphics   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2725] New modules for alignment graphics   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2725] New modules for alignment graphics   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15296] bioperl-live/trunk/t/RemoteDB/HIV/HIVQuery.t: Exception test failing, marking as a TODO for now   Christopher John Fields
• [Bioperl-guts-l] [15297] bioperl-ext/trunk: Bump to 1.007 (similar to trunk)   Christopher John Fields
• [Bioperl-guts-l] [15298] bioperl-live/trunk/t/SeqIO/abi.t: Should use full version   Christopher John Fields
• [Bioperl-guts-l] [15299] bioperl-live/trunk: Patch from Mark Jensen.   Christopher John Fields
• [Bioperl-guts-l] [15300] bioperl-live/branches/branch-1-6: Sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15301] bioperl-live/tags/bioperl-1-6-RC2/: Set tag for RC2   Christopher John Fields
• [Bioperl-guts-l] [15302] bioperl-live/trunk/Bio/DB/GFF/Aggregator/orf.pm: * use base   Christopher John Fields
• [Bioperl-guts-l] [15303] bioperl-live/branches/branch-1-6/Bio/DB/GFF/Aggregator/orf.pm: Sync that last bit with trunk.   Christopher John Fields
• [Bioperl-guts-l] [15304] bioperl-live/branches/branch-1-6/Build.PL: Resolve conflict (can' t directly merge since trunk and branch have slightly different deps)   Christopher John Fields
• [Bioperl-guts-l] [15305] bioperl-live/tags/bioperl-1-6-RC2/: deleting useless tag, will recreate in a moment   Christopher John Fields
• [Bioperl-guts-l] [15306] bioperl-live/tags/bioperl-1-6-RC2/: retag RC2   Christopher John Fields
• [Bioperl-guts-l] [15307] bioperl-live/trunk/t/Map/Map.t: bulletproof test ( remote data has changed slightly)   Christopher John Fields
• [Bioperl-guts-l] [15308] bioperl-live/branches/branch-1-6/t/Map/Map.t: Sync with trunk.   Christopher John Fields
• [Bioperl-guts-l] [Bug 2695] Incorrect processing of ampersand gt/lt entities   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2726] New: ace file IO   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2726] ace file IO   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2726] ace file IO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15309] bioperl-dev/: create developer directory for untested/unstable code   Christopher John Fields
• [Bioperl-guts-l] [15310] bioperl-live/trunk/Bio/Assembly/IO/phrap.pm: Seq->LocatableSeq ( Seqs do not have start/end).   Christopher John Fields
• [Bioperl-guts-l] [15311] bioperl-live/trunk/Changes: Minor edits   Christopher John Fields
• [Bioperl-guts-l] [15312] bioperl-live/trunk: * Assembly. t - warnings are due to the parser not actually parsing sequences (?!?).   Christopher John Fields
• [Bioperl-guts-l] [15313] bioperl-run/trunk: Catch version, skip tests if version isn' t supported yet (Clustalw 2.0, fo instance)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2728] New: [TODO] Update Bio::Run::Alignment::ClustalW to support ClustalW 2.0   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15314] bioperl-run/trunk/t/Ensembl.t: Getting a failed test using latest EnsEMBL perl API; TODO' ing the failed test for now.   Christopher John Fields
• [Bioperl-guts-l] [15315] bioperl-run/trunk/t/Ensembl.t: Don' t todo tests that work for other people - it causes test failure; reverted and changed test to handle presumed difference in Bio:: EnsEMBL versions   Senduran Balasubramaniam
  • [Bioperl-guts-l] [15315] bioperl-run/trunk/t/Ensembl.t: Don' t todo tests that work for other people - it causes test failure; reverted and changed test to handle presumed difference in Bio:: EnsEMBL versions   Chris Fields
    • [Bioperl-guts-l] [15315] bioperl-run/trunk/t/Ensembl.t: Don' t todo tests that work for other people - it causes test failure; reverted and changed test to handle presumed difference in Bio:: EnsEMBL versions   Sendu Bala
      • [Bioperl-guts-l] [15315] bioperl-run/trunk/t/Ensembl.t: Don' t todo tests that work for other people - it causes test failure; reverted and changed test to handle presumed difference in Bio:: EnsEMBL versions   Chris Fields
• [Bioperl-guts-l] [15316] bioperl-run/trunk: * convert to Bio::Root::Test   Christopher John Fields
• [Bioperl-guts-l] [15317] bioperl-run/trunk/t: * convert to Bio::Root::Test   Christopher John Fields
• [Bioperl-guts-l] [15318] bioperl-live/trunk/Bio/Root/Test.pm: * add requires_executable and requires_env to Bio::Root::Test ( for bioperl-run)   Christopher John Fields
• [Bioperl-guts-l] [15319] bioperl-run/trunk/t: * convert over to Bio::Root:: Test and update some to use new test_skip parameters   Christopher John Fields
• [Bioperl-guts-l] [15320] bioperl-run/trunk/t: requires not required   Christopher John Fields
• [Bioperl-guts-l] [Bug 2354] Bio::SeqIO::phd enhancement   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2354] Bio::SeqIO::phd enhancement   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] [15321] bioperl-live/trunk/Bio/SeqIO/phd.pm: [bug 2354]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2354] Bio::SeqIO::phd enhancement   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] [15322] bioperl-live/trunk/Bio/Root/Test.pm: * add diagnostics during run for requires_executable and requires_env   Christopher John Fields
• [Bioperl-guts-l] [15323] bioperl-run/trunk/t: * finish up bioperl-run conversion   Christopher John Fields
  • [Bioperl-guts-l] [15323] bioperl-run/trunk/t: * finish up bioperl-run conversion   Sendu Bala
    • [Bioperl-guts-l] [15323] bioperl-run/trunk/t: * finish up bioperl-run conversion   Chris Fields
      • [Bioperl-guts-l] [15323] bioperl-run/trunk/t: * finish up bioperl-run conversion   Sendu Bala
      • [Bioperl-guts-l] [15323] bioperl-run/trunk/t: * finish up bioperl-run conversion   Chris Fields
• [Bioperl-guts-l] [15324] bioperl-live/trunk/t/SeqIO: [CPAN Testers]   Christopher John Fields
• [Bioperl-guts-l] [15325] bioperl-live/trunk/t/Biblio/Biblio.t: [CPAN Testers]   Christopher John Fields
• [Bioperl-guts-l] [15326] bioperl-run/trunk/t/AnalysisFactory_soap.t: TODO failing test ( problem with SOAP protocol)   Christopher John Fields
• [Bioperl-guts-l] [15327] bioperl-run/trunk/t/Pise.t: Actually make tests complete ( not skipped if there is a job error, so tests abort prematurely)   Christopher John Fields
• [Bioperl-guts-l] [15328] bioperl-run/trunk/t/AnalysisFactory_soap.t: Don't TODO the test, actually attempt to run it and check for an error, then report the error if it fails.   Christopher John Fields
• [Bioperl-guts-l] [15329] bioperl-db/trunk/t: * convert over to Bio::Root::Test   Christopher John Fields
• [Bioperl-guts-l] [15330] bioperl-db/trunk: [bug 2573]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2573] Ontology tests failing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15331] bioperl-db/trunk/t: Bio::Root::Test relies on fall-back modules   Senduran Balasubramaniam
• [Bioperl-guts-l] [15332] bioperl-db/trunk/t/Test.pm: Test.pm no longer used   Senduran Balasubramaniam
• [Bioperl-guts-l] [15333] bioperl-db/trunk/t: '.' not required in lib   Senduran Balasubramaniam
• [Bioperl-guts-l] [15334] bioperl-run/trunk/t/Clustalw.t: corrected number of tests; output to a temp file   Senduran Balasubramaniam
• [Bioperl-guts-l] [15335] bioperl-run/trunk/t/Hmmer.t: test_output_file() creates an empty file, but it must be unlinked before hmmbuild will work   Senduran Balasubramaniam
• [Bioperl-guts-l] [15336] bioperl-run/trunk/t/MAFFT.t: removed syntactical nonsense that broke the test   Senduran Balasubramaniam
• [Bioperl-guts-l] [15337] bioperl-run/trunk: removed extraneous use lib lines   Senduran Balasubramaniam
• [Bioperl-guts-l] [15338] bioperl-run/trunk/Makefile.PL: revert mistaken commit   Senduran Balasubramaniam
• [Bioperl-guts-l] [15339] bioperl-live/trunk/Bio/Root/Test.pm: minor doc improvements   Senduran Balasubramaniam
  • [Bioperl-guts-l] [15339] bioperl-live/trunk/Bio/Root/Test.pm: minor doc improvements   Chris Fields
• [Bioperl-guts-l] [Bug 2514] Run tests with binaries installed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2515] GenBank XML parser   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 2615] Argument inconsistency in Bio::SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2354] Bio::SeqIO::phd enhancement   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15340] bioperl-live/trunk/Makefile.PL: removed this stub now that people have had time to adjust   Senduran Balasubramaniam
• [Bioperl-guts-l] [15341] bioperl-run/trunk/Makefile.PL: removed this stub now that people have had time to adjust   Senduran Balasubramaniam
• [Bioperl-guts-l] [15342] bioperl-db/trunk/Makefile.PL: removed this stub now that people have had time to adjust   Senduran Balasubramaniam
• [Bioperl-guts-l] [15343] bioperl-network/trunk/Makefile.PL: removed this stub now that people have had time to adjust   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2730] New: bp_load_ontology ISBN title parsing error in OBO format   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2730] bp_load_ontology ISBN title parsing error in OBO format   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15344] bioperl-pise/: create bioperl-pise repo to house former bioperl-run Pise modules   Christopher John Fields
• [Bioperl-guts-l] [15345] bioperl-pise/trunk/: create bioperl-pise repo to house former bioperl-run Pise modules   Christopher John Fields
• [Bioperl-guts-l] [15346] bioperl-live/trunk: Fixed bug in Bio::DB:: Fasta regarding the way the sequence length is calculated ( produced erroneous sequence length when truncated sequences were generated from full sequences ).   Florent E Angly
• [Bioperl-guts-l] [15347] bioperl-live/trunk/Bio/Seq/SeqWithQuality.pm: Made Bio::Seq:: SeqWithQuality do its sanity checks on Bio::SeqI and Bio:: PrimarySeqI instead of Bio::Seq and Bio::PrimarySeq.   Florent E Angly
• [Bioperl-guts-l] [15348] bioperl-pise/trunk: Move Pise modules over to bioperl-pise   Christopher John Fields
• [Bioperl-guts-l] [15349] bioperl-pise/trunk/Bio/Tools/Run: Move Pise modules over to bioperl-pise   Christopher John Fields
• [Bioperl-guts-l] [15350] bioperl-pise/trunk: Move Pise modules over to bioperl-pise   Christopher John Fields
• [Bioperl-guts-l] [15351] bioperl-run/trunk/t/Pise.t: Remove Pise modules and tests ( moved into bioperl-pise)   Christopher John Fields
• [Bioperl-guts-l] [15352] bioperl-run/trunk/Bio/Tools/Run: Remove Pise modules and tests ( moved into bioperl-pise)   Christopher John Fields
• [Bioperl-guts-l] [15353] bioperl-live/trunk/Bio/Seq/SeqWithQuality.pm: Just a little bit of cleaning in Bio::Seq::SeqWithQuality   Florent E Angly
• [Bioperl-guts-l] [15354] bioperl-run/trunk/Bio/Tools/Run/AnalysisFactory/Pise.pm: Remove Pise-related module (moved into bioperl-pise)   Christopher John Fields
• [Bioperl-guts-l] [15355] bioperl-pise/trunk/Bio/Tools/Run: Moved Pise-related module over to bioperl-pise   Christopher John Fields
• [Bioperl-guts-l] [15356] bioperl-run/trunk/examples/: Remove Pise-related examples ( moved into bioperl-pise)   Christopher John Fields
• [Bioperl-guts-l] [15357] bioperl-pise/trunk: Moved Pise-related examples over to bioperl-pise   Christopher John Fields
• [Bioperl-guts-l] [15358] bioperl-run/trunk/DEPENDENCIES: Add DEPENDENCIES file.   Christopher John Fields
• [Bioperl-guts-l] [15359] bioperl-run/trunk/Build.PL: Remove Pise-related stuff, update with other dependencies   Christopher John Fields
• [Bioperl-guts-l] [15360] bioperl-run/trunk: * small updates   Christopher John Fields
• [Bioperl-guts-l] [15361] bioperl-live/trunk/Bio/SeqIO/phd.pm: [bug 2354]   Christopher John Fields
• [Bioperl-guts-l] [15362] bioperl-live/trunk/maintenance: small updates   Christopher John Fields
• [Bioperl-guts-l] [15363] bioperl-live/trunk/Build.PL: * use the same executable name running tests; don't assume it is named ' perl'   Christopher John Fields
• [Bioperl-guts-l] [15364] bioperl-live/branches/branch-1-6: Sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [15365] bioperl-live/trunk/t/RemoteDB/HIV/HIV.t: * must eval each remote DB check and skip   Christopher John Fields
• [Bioperl-guts-l] [15366] bioperl-live/trunk/t/RemoteDB/HIV/HIV.t: * reduce failed test output   Christopher John Fields
• [Bioperl-guts-l] [15367] bioperl-live/trunk/t/RemoteDB/HIV/HIV.t: use lives_ok instead of eval, and skip based on $@   Christopher John Fields
• [Bioperl-guts-l] [15368] bioperl-live/trunk/Bio/Seq/SeqWithQuality.pm: add comma, was getting warnings with tests   Christopher John Fields
• [Bioperl-guts-l] [15369] bioperl-live/branches/branch-1-6: Sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [15370] bioperl-live/trunk/t/Biblio/eutils.t: requires XML::Twig   Christopher John Fields
• [Bioperl-guts-l] [15371] bioperl-run/trunk: Bio::Tools:: TigrAssembler improvement to allow to submit quality scores that are not in the same object as the sequences   Florent E Angly
• [Bioperl-guts-l] [Bug 2732] New: Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2732] Bio::DB::HIV failing test at get_Stream_by_acc   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15372] bioperl-live/trunk/DEPRECATED: * Update with Bio::Seq:: SeqWithQuality, Bio::DB::GDB   Christopher John Fields
• [Bioperl-guts-l] [15373] bioperl-live/trunk: * tweak regexes to properly catch MEGABLAST ( per Scott Markel)   Christopher John Fields
• [Bioperl-guts-l] [15374] bioperl-live/trunk/Bio/Tools/Run: Don't quotemeta if using Windows   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 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15375] bioperl-live/trunk/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: quenched "nonnumeric comparison" error when running under -w   Lincoln Stein
• [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] [15376] bioperl-live/trunk/Build.PL: * do not run live database tests ( including BDB) unless indicated   Christopher John Fields
• [Bioperl-guts-l] [15377] bioperl-live/trunk: Should be Bio::Seq::Quality, not a simple Bio:: Seq   Christopher John Fields
• [Bioperl-guts-l] [15378] bioperl-live/trunk/Bio/Seq/Quality.pm: speling iz fun-damental   Christopher John Fields
• [Bioperl-guts-l] [Bug 1986] SearchIO::blast mixes up hits where duplicate accessions are present   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15379] bioperl-live/trunk: GDB service is no longer available, modules removed from distribution (we can revive if someone else hosts it) .   Christopher John Fields
• [Bioperl-guts-l] [15380] bioperl-live/trunk/t/RemoteDB/HIV/HIVQuery.t: remove debugging counter check   Christopher John Fields
• [Bioperl-guts-l] [15381] bioperl-live/trunk: Updates   Christopher John Fields
• [Bioperl-guts-l] [15382] bioperl-live/trunk: HIV database updates   Christopher John Fields
• [Bioperl-guts-l] [15383] bioperl-live/branches/branch-1-6: Sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [15384] bioperl-live/trunk/t/RemoteDB/HIV/HIV.t: work around brittle test, which appears to be a server-side issue   Christopher John Fields
• [Bioperl-guts-l] [15385] bioperl-live/branches/branch-1-6/t/RemoteDB/HIV/HIV.t: Carry over test change from main trunk   Christopher John Fields
• [Bioperl-guts-l] [15386] bioperl-live/trunk/t/SearchIO/blastxml.t: fix blastxml skipped test count (thanks to Nathan Haigh)   Christopher John Fields
• [Bioperl-guts-l] [15387] bioperl-live/trunk/Bio/DB/MeSH.pm: throw exception when description is not defined   Christopher John Fields
• [Bioperl-guts-l] [15388] bioperl-live/branches/branch-1-6: carry over test fixes from trunk   Christopher John Fields
• [Bioperl-guts-l] [15389] bioperl-live/tags/bioperl-1-6-RC3/: tagging RC3   Christopher John Fields
• [Bioperl-guts-l] [15390] bioperl-live/tags/bioperl-1-6-RC3/: tagged RC3 too early ( need to update a few files)   Christopher John Fields
• [Bioperl-guts-l] [15391] bioperl-live/branches/branch-1-6/Bio/Root: Inc.   Christopher John Fields
• [Bioperl-guts-l] [15392] bioperl-live/tags/bioperl-1-6-RC3/: tagging RC3 (again)   Christopher John Fields
• [Bioperl-guts-l] [15393] bioperl-live/trunk/t/LocalDB: ActivePerl doesn't emulate open(FOO, '-|') yet   Christopher John Fields
• [Bioperl-guts-l] [15394] bioperl-live/trunk/t/LocalDB: use Bio::Root::Test syntax   Senduran Balasubramaniam
• [Bioperl-guts-l] [15395] bioperl-live/trunk/t/SeqIO/phd.t: comment out bad test (shouldn' t test a fixed attribute against a volatile value)   Christopher John Fields
• [Bioperl-guts-l] [15396] bioperl-live/trunk/t: tests require URI::Escape   Christopher John Fields
• [Bioperl-guts-l] [15397] bioperl-live/trunk: Add float_eq() for comparing floating point values (such as evalue, pvale, etc)   Christopher John Fields
• [Bioperl-guts-l] [15398] bioperl-live/trunk/t/SeqIO/asciitree.t: * test out minor change with outfile to see if interpolation is messing up writing to file   Christopher John Fields
• [Bioperl-guts-l] [15399] bioperl-live/trunk/t/Tree/TreeIO/phyloxml.t: remove old Test:: More cruft (and wondering if we should allow a callback test for Bio::Root: :Test)   Christopher John Fields
• [Bioperl-guts-l] [15400] bioperl-live/trunk: * add optional version tracking to deprecated() , along with tests   Christopher John Fields
• [Bioperl-guts-l] [15401] bioperl-live/trunk/t/RemoteDB/SeqRead_fail.t: * TAP count off if tests fail when using pipes, switch to using tempfile instead   Christopher John Fields
• [Bioperl-guts-l] [15402] bioperl-live/trunk: float_eq -> is_float_eq   Christopher John Fields
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2735] New: bp_load_gff.pl will not shut up   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2735] bp_load_gff.pl will not shut up   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2735] bp_load_gff.pl will not shut up   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15403] bioperl-live/trunk/Build.PL: Bump Data::Stag version to 0. 11 to fix warnings   Christopher John Fields
• [Bioperl-guts-l] [15404] bioperl-live/trunk: AnnotationFactor fixes; TODO now works   Christopher John Fields
• [Bioperl-guts-l] [15405] bioperl-live/trunk: make phrap less noisy yet still maintain a TODO   Christopher John Fields
• [Bioperl-guts-l] [15406] bioperl-live/trunk: is_float_eq => float_is (final version?)   Christopher John Fields
• [Bioperl-guts-l] [15407] bioperl-live/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [Bug 2736] New: Bio::DB::EUtilities::esearch fails when there is only one result   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2736] Bio::DB::EUtilities::esearch fails when there is only one result   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15408] bioperl-live/trunk/t/ClusterIO/ClusterIO.t: tests require Time:: HiRes (first available in perl 5.7.3)   Christopher John Fields
• [Bioperl-guts-l] [15409] bioperl-live/trunk/Bio/DB/Query/HIVQuery.pm: fixed ids() method to really clear the hash upon set with an empty   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2737] New: t/Root/Utilities test is fooled by softlinks to /usr/bin/gunzip   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2737] t/Root/Utilities test is fooled by softlinks to /usr/bin/gunzip   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2737] t/Root/Utilities test is fooled by softlinks to /usr/bin/gunzip   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2737] t/Root/Utilities test is fooled by softlinks to /usr/bin/gunzip   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15410] bioperl-live/trunk/t/LocalDB/SeqFeature.t: Test count off, now passes   Christopher John Fields
• [Bioperl-guts-l] [15411] bioperl-live/trunk/Bio/Root/Utilities.pm: don' t mistake soft links with actual exe   Christopher John Fields
  • [Bioperl-guts-l] [15411] bioperl-live/trunk/Bio/Root/Utilities.pm: don' t mistake soft links with actual exe   Sendu Bala
    • [Bioperl-guts-l] [15411] bioperl-live/trunk/Bio/Root/Utilities.pm: don' t mistake soft links with actual exe   Chris Fields
• [Bioperl-guts-l] [15412] bioperl-live/trunk/Bio/SeqFeature/Collection.pm: close file before unlinking   Christopher John Fields
• [Bioperl-guts-l] [15413] bioperl-live/trunk/Bio/Root/Utilities.pm: [bug 2737] \n* revert Utilities commit per bug report (doesn' t take links to non-PATH exes into consideration)   Christopher John Fields
• [Bioperl-guts-l] [15414] bioperl-live/trunk/Bio/SeqFeature/Collection.pm: * test passes with SUPER::DESTROY tailcall (needs checking on other OS's, may need to revert)   Christopher John Fields
  • [Bioperl-guts-l] [15414] bioperl-live/trunk/Bio/SeqFeature/Collection.pm: * test passes with SUPER::DESTROY tailcall (needs checking on other OS's, may need to revert)   Chris Fields
• [Bioperl-guts-l] [15415] bioperl-live/branches/branch-1-6: * delete Bio::DB::SeqFeature:: Store::DBI::Pg per Scott Cain   Christopher John Fields
• [Bioperl-guts-l] [15416] bioperl-live/branches/branch-1-6: * sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15417] bioperl-live/trunk/t/RemoteDB: * fix for volatile test data   Christopher John Fields
• [Bioperl-guts-l] [15418] bioperl-live/branches/branch-1-6: * sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15419] bioperl-db/branches/branch-1-6/: create 1.6 branch for bioperl-db   Christopher John Fields
• [Bioperl-guts-l] [15420] bioperl-run/branches/branch-1-6/: create 1.6 branch for bioperl-run   Christopher John Fields
• [Bioperl-guts-l] [15421] bioperl-network/branches/branch-1-6/: create 1. 6 branch for bioperl-network   Christopher John Fields
• [Bioperl-guts-l] [15422] bioperl-live/trunk/Bio/DB/BioFetch.pm: get rid of undef warnings popping up   Christopher John Fields
• [Bioperl-guts-l] [15423] bioperl-live/branches/branch-1-6/Bio/DB/BioFetch.pm: sync last commit   Christopher John Fields
• [Bioperl-guts-l] [15424] bioperl-live/tags/bioperl-1-6-RC4/: Tagging RC4   Christopher John Fields
• [Bioperl-guts-l] [Bug 2739] New: using nonstandard characters in protein alignment results in residue count warning   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2739] using nonstandard characters in protein alignment results in residue count warning   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2739] using nonstandard characters in protein alignment results in residue count warning   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2739] using nonstandard characters in protein alignment results in residue count warning   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15425] bioperl-network/trunk/t: Updated versions   Brian Osborne
• [Bioperl-guts-l] [15426] bioperl-network/trunk/t/Graph-Articulation.x: Updated versions   Brian Osborne
• [Bioperl-guts-l] [15427] bioperl-network/trunk/t: Add Test modules   Brian Osborne
• [Bioperl-guts-l] [15428] bioperl-network/trunk/BUGS: Update   Brian Osborne
• [Bioperl-guts-l] [15429] bioperl-network/trunk/t/lib: added remaining Test fall-back modules   Senduran Balasubramaniam
• [Bioperl-guts-l] [15430] bioperl-network/trunk/t: removed extraneous syntax; better use of Bio::Root::Test syntax   Senduran Balasubramaniam
• [Bioperl-guts-l] [15431] bioperl-live/trunk/Bio/Root/Build.pm: corrected Bioperl -> BioPerl   Senduran Balasubramaniam
• [Bioperl-guts-l] [15432] bioperl-network/branches/branch-1-6: sync with network trunk   Christopher John Fields
• [Bioperl-guts-l] [15433] bioperl-network/trunk/t/Edge.t: Remove superfluous use_ok   Brian Osborne
• [Bioperl-guts-l] [15434] bioperl-network/trunk/t/IO_dip_tab.t: Remove superfluous use_ok   Brian Osborne
• [Bioperl-guts-l] [15435] bioperl-network/trunk/t/IO_psi10.t: Minor edit   Brian Osborne
• [Bioperl-guts-l] [15436] bioperl-network/branches/branch-1-6/Build.PL: Have minimal version for branch be 1.5.9 RC1, designate this as RC1   Christopher John Fields
• [Bioperl-guts-l] [15437] bioperl-live/trunk/Bio: Minor cleaning   Florent E Angly
  • [Bioperl-guts-l] [15437] bioperl-live/trunk/Bio: Minor cleaning   Chris Fields
• [Bioperl-guts-l] [15438] bioperl-live/trunk/scripts/Bio-DB-GFF/genbank2gff3.PLS: added Don Gilbert' s patch to improve species and Annotation TagTree handling   Scott Cain
• [Bioperl-guts-l] [15439] bioperl-live/trunk: Fixed bug when compressing/ decompressing files with spaces in their name   Florent E Angly
• [Bioperl-guts-l] [15440] bioperl-live/trunk/Bio/DB/SeqFeature/Store/LoadHelper.pm: temporary directories are now removed immediately, rather than after process completes   Lincoln Stein
• [Bioperl-guts-l] [15441] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store/LoadHelper .pm: cleanup temporary files at DESTROY time rather than at process exit time   Lincoln Stein
  • [Bioperl-guts-l] [15441] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store/LoadHelper .pm: cleanup temporary files at DESTROY time rather than at process exit time   Chris Fields
    • [Bioperl-guts-l] [15441] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store/LoadHelper .pm: cleanup temporary files at DESTROY time rather than at process exit time   Lincoln Stein
• [Bioperl-guts-l] [15442] bioperl-live/trunk/Bio/DB/HIV/HIVQueryHelper.pm: added <=> to legal query chars   Mark Allen Jensen
• [Bioperl-guts-l] [15443] bioperl-live/branches/branch-1-6/Bio/Root: Bump version to 1. 6 for final release.   Christopher John Fields
• [Bioperl-guts-l] [15441] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store/LoadHelper .pm: cleanup temporary files at DESTROY time rather than at process exit time   Chris Fields
• [Bioperl-guts-l] [15444] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store/LoadHelper .pm: * revert r15441 for the time being (SeqFeature. t tests failing with Mac OS X, perl 5.10)   Christopher John Fields
• [Bioperl-guts-l] [15445] bioperl-live/tags/bioperl-release-1-6/: Tagging the final 1. 6 release.   Christopher John Fields
• [Bioperl-guts-l] [15446] bioperl-live/trunk/t/LocalDB/Registry.t: requires BerkeleyDB, thanks to Chad Davis for working that out!   Christopher John Fields
• [Bioperl-guts-l] [15447] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm: changed attribute searching behavior to be consistent with in-memory adaptor   Lincoln Stein
• [Bioperl-guts-l] [15448] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm: turned off debugging!   Lincoln Stein
• [Bioperl-guts-l] [15449] bioperl-run/trunk/Bio/Tools/Run/Alignment/MAFFT.pm: catch version if it contains alphanumeric   Christopher John Fields
• [Bioperl-guts-l] [15450] bioperl-run/trunk/t: * TODO failing AnalysisFactory_soap.t test ( appears to be a protocol issue)   Christopher John Fields
• [Bioperl-guts-l] [15451] bioperl-run/trunk/t/TCoffee.t: * newer versions of t_coffee failing this test, may check pre-Bio::Root:: Test version to see if it passes   Christopher John Fields
• [Bioperl-guts-l] [15452] bioperl-run/trunk/t/TCoffee.t: tweak error message   Christopher John Fields
• [Bioperl-guts-l] [15453] bioperl-live/trunk/Bio/DB/Query/HIVQuery.pm: annotations no longer lost to bit bucket   Mark Allen Jensen
• [Bioperl-guts-l] [15454] bioperl-live/trunk/Bio/DB/HIV/lanl-schema.xml: normalized ( lc and _ for spaces) all annotation keys   Mark Allen Jensen
• [Bioperl-guts-l] [15455] bioperl-run/trunk: small tweaks to primer3 ( should try getting this to recognize 'primer3_core')   Christopher John Fields
• [Bioperl-guts-l] [15456] bioperl-run/branches/branch-1-6: sync with run trunk   Christopher John Fields
• [Bioperl-guts-l] [15457] bioperl-db/tags/bioperl-1-6-RC1/: tag RC1   Christopher John Fields
• [Bioperl-guts-l] [15458] bioperl-run/tags/bioperl-1-6-RC1/: tag RC1   Christopher John Fields
• [Bioperl-guts-l] [15459] bioperl-network/tags/bioperl-1-6-RC1/: tag RC1   Christopher John Fields
• [Bioperl-guts-l] [15460] bioperl-run/branches/branch-1-6/Build.PL: forgot to change versioning, will retag   Christopher John Fields
• [Bioperl-guts-l] [15461] bioperl-db/branches/branch-1-6/Build.PL: forgot to change version, will retag   Christopher John Fields
• [Bioperl-guts-l] [15462] bioperl-network/branches/branch-1-6/Build.PL: Forgot to change version, will retag   Christopher John Fields
• [Bioperl-guts-l] [15463] bioperl-run/tags/bioperl-1-6-RC1/: remove (to be retagged)   Christopher John Fields
• [Bioperl-guts-l] [15464] bioperl-db/tags/bioperl-1-6-RC1/: remove (to be retagged)   Christopher John Fields
• [Bioperl-guts-l] [15465] bioperl-network/tags/bioperl-1-6-RC1/: remove (to be retagged)   Christopher John Fields
• [Bioperl-guts-l] [15466] bioperl-network/tags/bioperl-1-6-RC1/: retagging   Christopher John Fields
• [Bioperl-guts-l] [15467] bioperl-db/tags/bioperl-1-6-RC1/: retag   Christopher John Fields
• [Bioperl-guts-l] [15468] bioperl-run/tags/bioperl-1-6-RC1/: retag   Christopher John Fields
• [Bioperl-guts-l] [15469] bioperl-live/trunk/scripts: added hivq.PLS: command-line interface to Bio::DB::HIV   Mark Allen Jensen
• [Bioperl-guts-l] [15470] bioperl-live/trunk/scripts/DB-HIV/hivq.PLS: unixize newlines ( whoops!)   Mark Allen Jensen
• [Bioperl-guts-l] [15471] bioperl-live/trunk/scripts/DB-HIV/hivq.PLS: propset svn:keywords   Mark Allen Jensen
• [Bioperl-guts-l] [15472] bioperl-live/trunk/t: fix tests failing via CPAN Testers due to differences in floating point precision   Christopher John Fields
• [Bioperl-guts-l] [Bug 2744] New: Bio::LocatableSeq end.   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2744] Bio::LocatableSeq end.   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2744] Bio::LocatableSeq end.   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2744] Bio::LocatableSeq end.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15473] bioperl-network/trunk/INSTALL: Change versions, minor edits   Brian Osborne
• [Bioperl-guts-l] [Bug 2514] Run tests with binaries installed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15474] bioperl-network/trunk/Build.PL: New version number   Brian Osborne
• [Bioperl-guts-l] [15475] bioperl-live/trunk/INSTALL: Update   Brian Osborne
• [Bioperl-guts-l] [15476] bioperl-run/trunk/t/Genemark.hmm.prokaryotic.t: add some flexibility for older model names   Christopher John Fields
• [Bioperl-guts-l] [15477] bioperl-run/trunk/t/Vista.t: comma causing tests to fail on some systems if Java/Vista is present   Christopher John Fields
• [Bioperl-guts-l] [Bug 2746] New: [TODO] Update TCoffee wrapper for later versions   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2746] [TODO] Update TCoffee wrapper for later versions   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2747] New: [TODO] Build.PL requirement for Bio::Root::Build needs to be eval'd   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2747] [TODO] Build.PL requirement for Bio::Root::Build needs to be eval'd   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15478] bioperl-run/trunk: partial fix for TCoffee version above v5 ( still breaking some tests)   Christopher John Fields
• [Bioperl-guts-l] [15479] bioperl-run/trunk/Bio/Tools/Run/Alignment/TCoffee.pm: remove debugging line   Christopher John Fields
• [Bioperl-guts-l] [15480] bioperl-run/trunk/Bio/Tools/Run/Alignment/TCoffee.pm: TCoffee now passes   Christopher John Fields
• [Bioperl-guts-l] [15481] bioperl-run/trunk/Build.PL: use eval to check for Bio::Root::Build, die gracefully   Christopher John Fields
• [Bioperl-guts-l] [15482] bioperl-db/trunk/Build.PL: use eval to check for Bio::Root::Build   Christopher John Fields
• [Bioperl-guts-l] [15483] bioperl-network/trunk/Build.PL: use eval to check for Bio::Root:: Build   Christopher John Fields
• [Bioperl-guts-l] [15484] bioperl-db/trunk/Build.PL: switch to a simple die   Christopher John Fields
• [Bioperl-guts-l] [15485] bioperl-run/trunk/Build.PL: switch to simple die   Christopher John Fields
• [Bioperl-guts-l] [15486] bioperl-run/branches/branch-1-6: syc with trunk   Christopher John Fields
• [Bioperl-guts-l] [15487] bioperl-run/branches/branch-1-6/Build.PL: branch-specific versioning   Christopher John Fields
• [Bioperl-guts-l] [15488] bioperl-db/branches/branch-1-6/Build.PL: branch-specific versioning   Christopher John Fields
• [Bioperl-guts-l] [15489] bioperl-network/branches/branch-1-6: sync with trunk, branch-specific versioning   Christopher John Fields

Last message date: Sat Jan 31 23:53:22 EST 2009
Archived on: Sat Jan 31 23:53:26 EST 2009

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