February 2009 Archives by date

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Starting: Sun Feb 1 00:08:24 EST 2009
Ending: Sat Feb 28 19:12:13 EST 2009
Messages: 135

• [Bioperl-guts-l] [Bug 2514] Run tests with binaries installed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15490] bioperl-db/trunk/Build.PL: no empty strings, unset port should be undef instead   Christopher John Fields
• [Bioperl-guts-l] [15491] bioperl-db/branches/branch-1-6/Build.PL: sync last commit   Christopher John Fields
• [Bioperl-guts-l] [15492] bioperl-live/trunk/Bio/Root: * version to 1.6.9 (pre-1.7)   Christopher John Fields
• [Bioperl-guts-l] [15493] bioperl-run/trunk/Build.PL: version to 1.6.9 (pre-1.7)   Christopher John Fields
• [Bioperl-guts-l] [15494] bioperl-db/trunk/Build.PL: version to 1.6.9 (pre-1.7)   Christopher John Fields
• [Bioperl-guts-l] [15495] bioperl-network/trunk/Build.PL: version to 1.6.9 (pre-1.7)   Christopher John Fields
• [Bioperl-guts-l] [15496] bioperl-run/trunk/Bio/Tools/Run/Ensembl.pm: Fix Bio::DB:: EUtilities (API changed considerably from 1.5.2)   Christopher John Fields
• [Bioperl-guts-l] [15497] bioperl-live/trunk/t/Annotation/Annotation.t: Shouldn' t test module until needed (runs into compilation error w/o URI::Escape)   Christopher John Fields
• [Bioperl-guts-l] [15498] bioperl-live/trunk/t/RemoteDB/HIV/HIVQueryHelper.t: changed case of 'coreceptor' to reflect new schema   Mark Allen Jensen
• [Bioperl-guts-l] [15499] bioperl-live/trunk/t/SeqIO/asciitree.t: catch odd error popping up on some OS's (IRIX for instance); may be a File ::Temp issue   Christopher John Fields
• [Bioperl-guts-l] [15500] bioperl-live/trunk/t/SeqFeature/SeqFeatCollection.t: * getting something akin to a ulimit crash with this via CPAN testers using perl 5 .8.0 (linux)   Christopher John Fields
• [Bioperl-guts-l] [15501] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store/DBI/mysql. pm: I guess remove this, it breaks some things, although I am not sure what happens on INNODB database tables   Jason Stajich
• [Bioperl-guts-l] [15502] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm: I guess remove this, it breaks some things, although I am not sure what happens on INNODB database tables   Jason Stajich
• [Bioperl-guts-l] [15503] bioperl-run/trunk/t/AnalysisFactory_soap.t: TODO now passes ( thanks to Mahmut Uludag and Martin Senger)   Christopher John Fields
• [Bioperl-guts-l] [15504] bioperl-live/trunk/Bio/Search/HSP/GenericHSP.pm: significance can be zero   Christopher John Fields
• [Bioperl-guts-l] [15505] bioperl-live/branches/branch-1-6: sync with main trunk HEAD   Christopher John Fields
• [Bioperl-guts-l] [15506] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store/DBI/mysql. pm: remove more MYISAM forcing   Jason Stajich
• [Bioperl-guts-l] [15507] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm: remove MYISAM directives   Jason Stajich
• [Bioperl-guts-l] [15508] bioperl-live/trunk/scripts/seqstats/gccalc.PLS: somre more total stats   Jason Stajich
• [Bioperl-guts-l] [15509] bioperl-live/trunk/Bio/Align/DNAStatistics.pm: handle some divide by zero problems   Jason Stajich
• [Bioperl-guts-l] [15510] bioperl-live/trunk/Bio/RangeI.pm: deal with empty intersection   Jason Stajich
• [Bioperl-guts-l] [15511] bioperl-live/trunk/Bio/Tree/Node.pm: removed automatic path contraction, see   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15512] bioperl-db/trunk/t/01dbadaptor.t: remove extraneous test which can throw the test count off by one if __dummy__ namespace is left over from aborted test run   Christopher John Fields
• [Bioperl-guts-l] [15513] bioperl-db/trunk/t/16obda.t: use test_input_file()   Christopher John Fields
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15514] bioperl-run/trunk/t: requires network connection to work   Christopher John Fields
• [Bioperl-guts-l] [Bug 2753] New: Unknown format of PAML output did not see seqtype in Yn00   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2755] New: Bad apropos/whatis entries in some manual pages.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15515] bioperl-live/branches/branch-1-6: adding brief descriptions to modules and scripts which lack them.   Dave Messina
• [Bioperl-guts-l] [15516] bioperl-live/trunk: merging r15515 to trunk from 1.6 branch   Dave Messina
• [Bioperl-guts-l] [Bug 2755] Bad apropos/whatis entries in some manual pages.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15517] bioperl-run/trunk/INSTALL.SKIP: skip ConfigData for now   Christopher John Fields
• [Bioperl-guts-l] [15518] bioperl-db/trunk/INSTALL.SKIP: skip ConfigData   Christopher John Fields
• [Bioperl-guts-l] [15519] bioperl-network/trunk/INSTALL.SKIP: skip ConfigData   Christopher John Fields
• [Bioperl-guts-l] [15520] bioperl-live/trunk/INSTALL.SKIP: skip ConfigData (for now)   Christopher John Fields
• [Bioperl-guts-l] [15521] bioperl-run/branches/branch-1-6: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15522] bioperl-db/branches/branch-1-6: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15523] bioperl-network/branches/branch-1-6/INSTALL.SKIP: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15524] bioperl-run/tags/bioperl-1-6-RC2/: tag next alpha, or RC, or whatever ya wanna call it   Christopher John Fields
• [Bioperl-guts-l] [15525] bioperl-db/tags/bioperl-1-6-RC2/: tag next alpha   Christopher John Fields
• [Bioperl-guts-l] [15526] bioperl-network/tags/bioperl-1-6-RC2/: tag next alpha   Christopher John Fields
• [Bioperl-guts-l] [15526] bioperl-network/tags/bioperl-1-6-RC2/: tag next alpha   Chris Fields
• [Bioperl-guts-l] [Bug 2756] New: t/IO_psi10.t doesn't use Bio::Network::Node but calls $node->proteins()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2756] t/IO_psi10.t doesn't use Bio::Network::Node but calls $node->proteins()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15527] bioperl-network/trunk/t/IO_psi10.t: [bug 2756]   Christopher John Fields
• [Bioperl-guts-l] [15528] bioperl-network/branches/branch-1-6/t/IO_psi10.t: sync last commit   Christopher John Fields
• [Bioperl-guts-l] [Bug 2756] t/IO_psi10.t doesn't use Bio::Network::Node but calls $node->proteins()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2757] New: DBI $sth->execute() with no error check in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2757] DBI $sth->execute() with no error check in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15529] bioperl-live/trunk: adding SeqIO support and tests for EMBL-format CDS records.   Dave Messina
• [Bioperl-guts-l] [Bug 2758] New: assemblyIO - can't read phredPhrap ace file with tagged repeats   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15530] bioperl-live/trunk/Bio/Root/IO.pm: now throws if non-filehandle provided for -FH arg   Mark Allen Jensen
• [Bioperl-guts-l] [15531] bioperl-live/trunk/Bio/TreeIO/newick.pm: semicolon issue   Christopher John Fields
• [Bioperl-guts-l] [15532] bioperl-live/trunk/Bio/TreeIO.pm: small typo   Christopher John Fields
• [Bioperl-guts-l] [15533] bioperl-live/trunk/Bio/SimpleAlign.pm: mark' s SimpleAlign code for inserting sequences   Christopher John Fields
• [Bioperl-guts-l] [15534] bioperl-live/trunk/t: add tests for semicolon issue   Christopher John Fields
• [Bioperl-guts-l] [15535] bioperl-run/trunk: allow either primer3 or primer3_core   Christopher John Fields
• [Bioperl-guts-l] [15536] bioperl-run/trunk/Bio/Tools/Run/Alignment/Clustalw.pm: fix for neg.   Christopher John Fields
• [Bioperl-guts-l] [15537] bioperl-live/trunk: fix TODO's for blastxml, add tests   Christopher John Fields
• [Bioperl-guts-l] [15538] bioperl-run/trunk: get Vista.t passing   Christopher John Fields
• [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] [Bug 2763] New: [TODO] Refactor Bio::FeatureIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15539] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Pg.pm: OK, it still doesn't pass several tests, but at least it now makes it through all the tests without dying--progress!   Scott Cain
• [Bioperl-guts-l] [15540] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Iterator.pm: calling finish on the statement handle before undefing it   Scott Cain
• [Bioperl-guts-l] [15541] bioperl-live/trunk/Bio/DB/SeqFeature/Segment.pm: adding refseq alias for ref per Sheldon's request   Scott Cain
• [Bioperl-guts-l] [Bug 2764] New: enhance SwissProt retreival by id using IDTracker   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2766] New: SeqUtils not copying SeqFeature tags   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2766] SeqUtils not copying SeqFeature tags   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15542] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Pg.pm: this still doesn't pass all tests but works fine with GBrowse1.   Scott Cain
• [Bioperl-guts-l] [15543] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Pg.pm: silencing a debugging message   Scott Cain
• [Bioperl-guts-l] [15544] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Pg.pm: silencing a debug message without the uninit variable   Scott Cain
• [Bioperl-guts-l] [15545] bioperl-live/trunk: reduced size of Pg adapter by inheriting from mysql adapter and removing redundant code ; regression tests pass if -temp flag is not used; need to test bulk loading   Lincoln Stein
• [Bioperl-guts-l] [15546] bioperl-live/trunk: postgres adapter passes all regression tests but no longer drives gbrowse.   Lincoln Stein
• [Bioperl-guts-l] [Bug 2773] New: Bio::Tree::Node gets destroyed even though it is still live   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15547] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Pg.pm: starting to fix key word searching--I thought this used to work   Scott Cain
• [Bioperl-guts-l] [15548] bioperl-live/trunk/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: fixed file format error checking to avoid throwing an exception on group lines   Lincoln Stein
• [Bioperl-guts-l] [15549] bioperl-live/trunk: adding pod FEEDBACK:Support section, with associated bioperl.lisp   Mark Allen Jensen
• [Bioperl-guts-l] [15550] bioperl-live/trunk: added test for case sensitivity, which Pg adapter fails; make sure that temp directory is not deleted prematurely for in-memory and berkeley adapters   Lincoln Stein
• [Bioperl-guts-l] [15551] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Pg.pm: fixed case-insensitive search; keyword search still broken   Lincoln Stein
• [Bioperl-guts-l] [15552] bioperl-db/trunk/Bio: adding FEEDBACK:Support section to pod   Mark Allen Jensen
• [Bioperl-guts-l] [15553] bioperl-ext/trunk/Bio/SeqIO/staden/read.pm: adding FEEDBACK: Support section to pod   Mark Allen Jensen
• [Bioperl-guts-l] [15554] bioperl-microarray/trunk/Bio/Expression: adding FEEDBACK: Support section to pod   Mark Allen Jensen
• [Bioperl-guts-l] [15555] bioperl-network/trunk/Bio/Network: adding FEEDBACK: Support section to pod   Mark Allen Jensen
• [Bioperl-guts-l] [15556] bioperl-pedigree/trunk/Bio/Pedigree: adding FEEDBACK: Support section to pod   Mark Allen Jensen
• [Bioperl-guts-l] [15557] bioperl-pipeline/trunk: adding FEEDBACK:Support section to pod   Mark Allen Jensen
• [Bioperl-guts-l] [15558] bioperl-run/trunk/Bio: adding FEEDBACK:Support section to pod   Mark Allen Jensen
• [Bioperl-guts-l] [15559] bioperl-live/trunk/bioperl.lisp: Id keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [15560] bioperl-live/trunk/bioperl.komodo: first pass at a Komodo BioPerl template file   Christopher John Fields
• [Bioperl-guts-l] [15561] bioperl-db/branches/branch-1-6/Bio: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15562] bioperl-network/trunk/t/Interaction.t: fix a failed test due to live core change (allows one to use network 1. 6 with bioperl-live if needed)   Christopher John Fields
• [Bioperl-guts-l] [15563] bioperl-network/branches/branch-1-6: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15564] bioperl-run/branches/branch-1-6: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [15565] bioperl-live/trunk/Bio/Root/IO.pm: allow IO::String   Christopher John Fields
• [Bioperl-guts-l] [15566] bioperl-network/branches/branch-1-6/Build.PL: bump version   Christopher John Fields
• [Bioperl-guts-l] [15567] bioperl-run/branches/branch-1-6/Build.PL: bump version   Christopher John Fields
• [Bioperl-guts-l] [15568] bioperl-db/branches/branch-1-6/Build.PL: bump version   Christopher John Fields
• [Bioperl-guts-l] [15569] bioperl-db/tags/release-1-6/: tag 1.6 release   Christopher John Fields
• [Bioperl-guts-l] [15570] bioperl-network/tags/release-1-6/: tag release   Christopher John Fields
• [Bioperl-guts-l] [15571] bioperl-run/tags/release-1-6/: tag release   Christopher John Fields
• [Bioperl-guts-l] [15572] bioperl-dev/trunk/: add trunk   Christopher John Fields
• [Bioperl-guts-l] [15573] bioperl-live/trunk: fixed Pg keyword searching to do an OR search rather than an AND search on multiple terms for compatibility with other adapters   Lincoln Stein
• [Bioperl-guts-l] [Bug 2766] SeqUtils not copying SeqFeature tags   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15574] bioperl-run/trunk/t/Primer3.t: fix test numbering   Christopher John Fields
• [Bioperl-guts-l] [15575] bioperl-run/branches/branch-1-6/t/Primer3.t: merge last commit to branch   Christopher John Fields
• [Bioperl-guts-l] [15576] bioperl-run/tags/release-1-6-1/: * new tagged release (1.6.1)   Christopher John Fields
• [Bioperl-guts-l] [15577] bioperl-live/trunk/Bio/DB/SeqFeature/Store/GFF3Loader.pm: added more error checking to gff3 parsing routines   Lincoln Stein
• [Bioperl-guts-l] [15578] bioperl-run/trunk/INSTALL: Update   Brian Osborne
• [Bioperl-guts-l] [15579] bioperl-network/trunk/INSTALL: Update   Brian Osborne
• [Bioperl-guts-l] [15580] bioperl-live/trunk/Bio/SeqIO/fastq.pm: unpack / split speed up   Albert Vilella
• [Bioperl-guts-l] [15581] bioperl-live/trunk/Bio/PopGen/Statistics.pm: simplify LD code a bit , we don't need to keep a running set for all pairs   Jason Stajich
• [Bioperl-guts-l] [15582] bioperl-live/branches/branch-1-6/Bio/PopGen/Statistics.pm: simplify LD code a bit, we aren't keeping running set for all pairs   Jason Stajich

Last message date: Sat Feb 28 19:12:13 EST 2009
Archived on: Sat Feb 28 19:12:17 EST 2009

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