June 2008 Archives by subject

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Starting: Mon Jun 2 16:05:55 EDT 2008
Ending: Mon Jun 30 19:02:51 EDT 2008
Messages: 99

• [Bioperl-guts-l] [14688] bioperl-live/trunk/Bio/Tree/NodePhyloXML.pm: start_element/ end_element clade   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14689] bioperl-live/trunk/Bio/TreeIO/PhyloXMLEventBuilder.pm: start_element/end_element clade   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14690] bioperl-live/trunk/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: fixed POD errors   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14691] bioperl-live/trunk/t/largepseq.t: fix number of tests   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14692] bioperl-live/trunk/t/DBCUTG.t: correct number of tests   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14693] bioperl-live/trunk/t/game.t: skip tests when XML:: Writer is not installed   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14694] bioperl-live/trunk/t/RestrictionIO.t: skip tests that need networking using the same logic that all other modules use .   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14695] bioperl-live/trunk/t/EUtilities.t: use uniform notice string when skipping network tests   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14696] bioperl-live/trunk/maintenance/pod.pl: point searches to bioperl-run assuming that it is at the same directory as bioperl-live   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14697] bioperl-live/trunk/Bio: fix POD errors   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14698] bioperl-live/trunk/Bio/Graphics/Glyph/xyplot.pm: fixed scale on xyplot so that scale values < 0 are rendered correctly   Lincoln Stein
• [Bioperl-guts-l] [14699] bioperl-live/trunk/Bio/Graphics/Glyph/xyplot.pm: fixed the positioning of the '0' coordinate on the scale so that it doesn' t clash with the midpoint coordinate   Lincoln Stein
• [Bioperl-guts-l] [14700] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: Change phyloxml to using libxml instead of SAX   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14701] bioperl-live/trunk/t: Change phyloxml to using libxml instead of SAX   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14702] bioperl-live/trunk/Bio/TreeIO/PhyloXMLEventBuilder.pm: Change phyloxml to using libxml instead of SAX   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14703] bioperl-live/trunk/t: Change phyloxml to using libxml instead of SAX   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14704] bioperl-live/trunk/Bio/Tree: phyloxml: next_tree and basic parsing of <clade>   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14705] bioperl-live/trunk/t/phyloxml.t: phyloxml: next_tree and basic parsing of <clade>   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14706] bioperl-live/trunk/t/phyloxml.t: requires_modules XML::LibXML   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14707] bioperl-live/trunk/t/phyloxml.t: requires_modules XML::LibXML   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14708] bioperl-live/trunk: fixing POD whitespaceissues   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14709] bioperl-run/trunk/Bio/Tools/Run: fixing POD whitespace issues   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14710] bioperl-live/trunk/Bio: POD fixes   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14711] bioperl-run/trunk/Bio/Tools/Run: POD fixes   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14712] bioperl-live/trunk: use function hash instead of if-else   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14713] bioperl-run/trunk/Bio/Tools/Run: POD fixes   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14714] bioperl-run/trunk/t: All tests pass now even if no binaries are installed.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14715] bioperl-run/trunk/Bio/Tools/Run: silence warnings   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14716] bioperl-live/trunk: Why is Bio::SeqFeature:: Annotated object creation downloading so.obo from sourceforge? This is an emergency fix disabling these tests if no network is available.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14717] bioperl-run/trunk: Added version() method.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14718] bioperl-live/trunk/Bio/Tree: New module TreePhyloXML. pm for phyloxml specific variables.   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14719] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: phyloxml: name, confidence   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14720] bioperl-live/trunk/t/phyloxml.t: test new module TreePhyloXML   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14721] bioperl-live/trunk: Removed TreePhyloXML.pm   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14722] bioperl-live/trunk/Bio/Tree/TreePhyloXML.pm: Removed TreePhyloXML. pm   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14723] bioperl-live/trunk/Bio/Tree/TreeI.pm: inherit from Bio::Root:: RootI instead of NodeI   Jason Stajich
• [Bioperl-guts-l] [14724] bioperl-live/trunk/Bio/Tree/TreeFunctionsI.pm: some whitespace cleanup   Jason Stajich
• [Bioperl-guts-l] [14725] bioperl-live/trunk/Bio/DB/Fasta.pm: doc expansion   Jason Stajich
• [Bioperl-guts-l] [14726] bioperl-live/trunk/Bio/SearchIO/blast.pm: bug 2517   Christopher John Fields
• [Bioperl-guts-l] [14727] bioperl-live/trunk/Bio/AlignIO/msf.pm: bug 2518   Christopher John Fields
• [Bioperl-guts-l] [14728] bioperl-live/trunk/Bio/Assembly/IO/ace.pm: bug 2519   Christopher John Fields
• [Bioperl-guts-l] [14729] bioperl-live/trunk: bug 2512 (Gene Ontology changes)   Christopher John Fields
• [Bioperl-guts-l] [14730] bioperl-live/trunk/Bio/Graphics/Glyph: added a bicolor_pivot option to the xyplot glyph to allow the color switch to occur at non-zero values   Lincoln Stein
• [Bioperl-guts-l] [14731] bioperl-live/trunk/Bio/Tools/GFF.pm: simplify list of special ID tags and their preferred order, still needs some more work; Indentation standardization from emacs   Jason Stajich
• [Bioperl-guts-l] [14732] bioperl-live/trunk/Bio/Tools/Genewise.pm: More GFF3 like output   Jason Stajich
• [Bioperl-guts-l] [14733] bioperl-live/trunk/Bio/Tools/Genewise.pm: set the ID, typo   Jason Stajich
• [Bioperl-guts-l] [14734] bioperl-live/trunk/Bio/Graphics/Glyph/minmax.pm: Bio::Graphics:: Glyph::minmax is the base class that defines midpoint(); fixed bug that mistakenly called SUPER::minmax()   Lincoln Stein
• [Bioperl-guts-l] [14735] bioperl-live/trunk/Bio/Tree: changed NodePhyloXML to AnnotatableNode   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14736] bioperl-live/trunk/Bio/Tree: changed NodePhyloXML to AnnotatableNode   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14737] bioperl-live/trunk/Bio/Tools/Glimmer.pm: bug 2423   Christopher John Fields
• [Bioperl-guts-l] [14738] bioperl-live/trunk/t/Genpred.t: bug 2423   Christopher John Fields
• [Bioperl-guts-l] [14739] bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm: avoid undefined warnings when start/end are empty.   Jason Stajich
• [Bioperl-guts-l] [14740] bioperl-experimental/: initial Perl6 code repository experiment   Jason Stajich
• [Bioperl-guts-l] [14741] bioperl-live/trunk: <property> via Bio::Annotation   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14742] bioperl-run/trunk/Bio/Tools/Run/Genemark.pm: bug 2523   Christopher John Fields
• [Bioperl-guts-l] [14743] bioperl-run/trunk: AAML parsing was failing on runmode=0 data ( usertree)   Jason Stajich
• [Bioperl-guts-l] [14744] bioperl-live/trunk/Bio/Tools/Phylo/PAML.pm: AAML parsing was failing on runmode=0 data (usertree)   Jason Stajich
• [Bioperl-guts-l] [14745] bioperl-live/trunk: <property> using id_source and id_ref   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14746] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: <property> using id_source and id_ref   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14747] bioperl-live/trunk: _to_string callback for AnnotatableNode and phyloxml   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [Bug 2423] Bio::Tools::Glimmer - frame support for Glimmer2/3 parser   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2423] Bio::Tools::Glimmer - frame support for Glimmer2/3 parser   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2423] Bio::Tools::Glimmer - frame support for Glimmer2/3 parser   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2504] Bug in Bio::SearchIO module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] New: Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2512] Patches for obo parser to recognize new relationships   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2513] creating a Bio::SeqFeature::Annotation object downloads the entire so.obo   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2513] creating a Bio::SeqFeature::Annotation object downloads the entire so.obo   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2513] New: creating a Bio::SeqFeature::Annotation object downloads the entire so.obo   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2514] New: Run tests with binaries installed   Chris Fields
• [Bioperl-guts-l] [Bug 2514] New: Run tests with binaries installed   bugzilla-daemon at portal.open-bio.org
• [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 2515] New: GenBank XML parser   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2517] New: Bio/SearchIO/blast.pm line 808 : Unmatched [ in regex;   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2518] New: Sequneces mis-aligned in msf format if some sequence names are longer than 20 characters   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2518] Sequneces mis-aligned in msf format if some sequence names are longer than 20 characters   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2518] Sequneces mis-aligned in msf format if some sequence names are longer than 20 characters   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2518] Sequneces mis-aligned in msf format if some sequence names are longer than 20 characters   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2519] Bio::Assembly::IO::ace allow for non "Contig\d" naming   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2519] New: Bio::Assembly::IO::ace allow for non "Contig\d" naming   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2522] New: Bio::Ontology::Ontology->get_all_terms() returns an empty list after reading an obo file.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2523] Bio::Tools::Run::Genemark should check for license warnings   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2523] Bio::Tools::Run::Genemark should check for license warnings   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2523] New: Bio::Tools::Run::Genemark should check for license warnings   bugzilla-daemon at portal.open-bio.org

Last message date: Mon Jun 30 19:02:51 EDT 2008
Archived on: Mon Jun 30 19:03:00 EDT 2008

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