September 2009 Archives by subject

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Starting: Tue Sep 1 03:13:39 EDT 2009
Ending: Wed Sep 30 16:45:17 EDT 2009
Messages: 254

• [Bioperl-guts-l] [16017] bioperl-dev/trunk: Bioperl minor mode for emacs   Mark Allen Jensen
• [Bioperl-guts-l] [16018] bioperl-dev/trunk/ide/emacs/bioperl-mode: - solved Emacs 21 compat issues   Mark Allen Jensen
• [Bioperl-guts-l] [16019] bioperl-dev/trunk/ide/emacs/bioperl-mode/dist: retarring on dev node   Mark Allen Jensen
• [Bioperl-guts-l] [16020] bioperl-dev/trunk/ide/emacs/bioperl-mode: fixed PERL5LIB parsing issue   Mark Allen Jensen
• [Bioperl-guts-l] [16021] bioperl-dev/branches/bioperl-mode-multipath-branch/: branch for working out multiple module path   Mark Allen Jensen
• [Bioperl-guts-l] [16022] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp: begin refactor of bioperl-module-path   Mark Allen Jensen
• [Bioperl-guts-l] [16023] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: not there yet, but closer   Mark Allen Jensen
• [Bioperl-guts-l] [16024] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: incremental commit   Mark Allen Jensen
• [Bioperl-guts-l] [16025] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: Extremely close now -   Mark Allen Jensen
• [Bioperl-guts-l] [16026] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: *beta*   Mark Allen Jensen
• [Bioperl-guts-l] [16027] bioperl-dev/branches/bioperl-mode-multipath-branch/dist: retarred multipath branch beta in branch dist   Mark Allen Jensen
• [Bioperl-guts-l] [16028] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: key fix to module cache loader   Mark Allen Jensen
• [Bioperl-guts-l] [16029] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: last patch requires this new initial setting   Mark Allen Jensen
• [Bioperl-guts-l] [16030] bioperl-dev/branches/bioperl-mode-multipath-branch/dist: retarred ( includes r16028 and r16029)   Mark Allen Jensen
• [Bioperl-guts-l] [16031] bioperl-live/trunk/Bio/LocatableSeq.pm: the no_* methods are deprecated in favor of num_*   Christopher John Fields
• [Bioperl-guts-l] [16032] bioperl-live/trunk/Changes: initial update for 1.6.1 ( not finished yet)   Christopher John Fields
• [Bioperl-guts-l] [16033] bioperl-live/trunk/Changes: finish up Changes for 1.6.1:wq   Christopher John Fields
• [Bioperl-guts-l] [16034] bioperl-live/trunk/t/Seq: num_*, not no_*   Christopher John Fields
• [Bioperl-guts-l] [16035] bioperl-live/trunk/t/Align/SimpleAlign.t: num_*, not no_*   Christopher John Fields
• [Bioperl-guts-l] [16036] bioperl-live/trunk/Bio/LocatableSeq.pm: add no_gaps deprecated stub , fix C&P sloppiness   Christopher John Fields
• [Bioperl-guts-l] [16037] bioperl-live/trunk/Changes: slight amplifications/1.6.1   Mark Allen Jensen
• [Bioperl-guts-l] [16038] bioperl-live/trunk/AUTHORS: tiling   Mark Allen Jensen
• [Bioperl-guts-l] [16038] bioperl-live/trunk/AUTHORS: tiling   Chris Fields
• [Bioperl-guts-l] [16039] bioperl-live/trunk/t/RemoteDB/SwissProt.t: idtracker may be down.   Christopher John Fields
• [Bioperl-guts-l] [16040] bioperl-live/trunk/AUTHORS: add Chase   Mark Allen Jensen
• [Bioperl-guts-l] [16041] bioperl-live/trunk/t/RemoteDB: fix volatile data test ( check for minimal but existing sequence length)   Christopher John Fields
• [Bioperl-guts-l] [16042] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: use assoc-string to allow case insensitive module names   Mark Allen Jensen
• [Bioperl-guts-l] [16043] bioperl-live/trunk/t/data/bug2862.pmr: remove newlines ( somehow these were added in)   Christopher John Fields
• [Bioperl-guts-l] [16044] bioperl-live/trunk/Bio/Index/Fasta.pm: Parse must start with '>' to identify sequence as FASTA   Christopher John Fields
• [Bioperl-guts-l] [16045] bioperl-live/trunk/Bio/Index/Fasta.pm: add comment about fix   Christopher John Fields
• [Bioperl-guts-l] [16046] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: omit nulls to admit trailing ::   Mark Allen Jensen
• [Bioperl-guts-l] [16047] bioperl-dev/branches/bioperl-mode-multipath-branch/dist: retarred multi-branch beta (gamma?)   Mark Allen Jensen
• [Bioperl-guts-l] [16048] bioperl-dev/trunk/ide/emacs/bioperl-mode/dist: omit nulls to admit trailing :: (EVERYwhere)   Mark Allen Jensen
• [Bioperl-guts-l] [16049] bioperl-dev/branches/bioperl-mode-multipath-branch/site-lisp/ bioperl-mode.el: omit nulls to admit trailing :: (EVERYwhere)   Mark Allen Jensen
• [Bioperl-guts-l] [16050] bioperl-dev/branches/bioperl-mode-multipath-branch/dist: retarred( ded) multipath branch...   Mark Allen Jensen
• [Bioperl-guts-l] [16051] bioperl-live/trunk/t/RemoteDB/EUtilities.t: volatile test fix ( NCBI changed webenv key length again)   Christopher John Fields
• [Bioperl-guts-l] [16052] bioperl-live/trunk/Bio/Nexml/Factory.pm: tweaks to get rid of warnings; note the TODO (should a Bio:: AlignIO be called there?)   Christopher John Fields
• [Bioperl-guts-l] [16053] bioperl-live/trunk/Bio/Nexml/Factory.pm: more tweaks and more TODO' s to note; should all caller's IDs be defined? Getting warnings in some cases that they aren't...   Christopher John Fields
• [Bioperl-guts-l] [16054] bioperl-live/trunk: fixed tiny typo   Lincoln Stein
• [Bioperl-guts-l] [16055] bioperl-live/trunk/Bio/DB: fixed test failure and warnings raised by cjf   Mark Allen Jensen
• [Bioperl-guts-l] [16056] bioperl-dev/branches/bioperl-mode-multipath-branch: updates, unit tests (really! see 'test.el'   Mark Allen Jensen
• [Bioperl-guts-l] [16057] bioperl-dev/tags/bioperl-mode-pre-multipath-merge/: tag the initially released version   Mark Allen Jensen
• [Bioperl-guts-l] [16058] bioperl-dev/trunk/ide/emacs/bioperl-mode: merge from branches/ bioperl-mode-multipath-branch   Mark Allen Jensen
• [Bioperl-guts-l] [16059] bioperl-dev/branches/bioperl-mode-multipath-branch/dist: retar the trunk distribution   Mark Allen Jensen
• [Bioperl-guts-l] [16060] bioperl-dev/trunk/ide/emacs/bioperl-mode: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [16061] bioperl-dev/branches/bioperl-mode-multipath-branch/dist: retar ( geez)   Mark Allen Jensen
• [Bioperl-guts-l] [16062] bioperl-dev/branches/bioperl-mode-multipath-branch/: purpose complete   Mark Allen Jensen
• [Bioperl-guts-l] [16063] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp: pretty pod formatting and fontification   Mark Allen Jensen
• [Bioperl-guts-l] [16064] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp/bioperl-init.el: improved syntax highlighting   Mark Allen Jensen
• [Bioperl-guts-l] [16065] bioperl-live/trunk: Fixed solexa mapping.   Christopher John Fields
• [Bioperl-guts-l] [16066] bioperl-live/trunk/Bio/Tree/TreeFunctionsI.pm: convert _clone to public method clone   Mark Allen Jensen
• [Bioperl-guts-l] [16067] bioperl-dev/trunk/ide/emacs/bioperl-mode/test/bioperl-mode-test.el: tracking source changes   Mark Allen Jensen
• [Bioperl-guts-l] [16068] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp: feeping creaturism (view module source func)   Mark Allen Jensen
• [Bioperl-guts-l] [16069] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp/bioperl-init.el: enforce Emacs 22   Mark Allen Jensen
• [Bioperl-guts-l] [16070] bioperl-dev/trunk/ide/emacs/bioperl-mode/dist: retarred distribution   Mark Allen Jensen
• [Bioperl-guts-l] [16071] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp/pod.el: Parse pod ourselves   Mark Allen Jensen
• [Bioperl-guts-l] [16072] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp: removed dependency on pod2text;   Mark Allen Jensen
• [Bioperl-guts-l] [16073] bioperl-dev/trunk/ide/emacs/bioperl-mode/dist: retarred (r16072)   Mark Allen Jensen
• [Bioperl-guts-l] [16074] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp/pod.el: parser tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16075] bioperl-dev/trunk/ide/emacs/bioperl-mode/dist: retarred (r16074)   Mark Allen Jensen
• [Bioperl-guts-l] [16076] bioperl-dev/trunk/ide/emacs/bioperl-mode/site-lisp: bug squishes   Mark Allen Jensen
• [Bioperl-guts-l] [16077] bioperl-dev/trunk/ide/emacs/bioperl-mode/dist: retarred (r16076)   Mark Allen Jensen
• [Bioperl-guts-l] [16078] bioperl-live/trunk/Bio/Search/HSP/FastaHSP.pm: verbosity should be the same as parent, not hard-coded   Christopher John Fields
• [Bioperl-guts-l] [16079] bioperl-live/trunk/Bio/Nexml/Factory.pm: untabify   Christopher John Fields
• [Bioperl-guts-l] [16080] bioperl-live/trunk: fix raw sequence tests (new variants weren' t working for some reason)   Christopher John Fields
• [Bioperl-guts-l] [16081] bioperl-live/trunk/Bio/SimpleAlign.pm: regarding bug 2911, trivial doc patch to SYNOPSIS section of Bio::SimpleAlign   Robert Buels
• [Bioperl-guts-l] [16082] bioperl-live/trunk/t/Align/SimpleAlign.t: a TODO test case for bug 2842   Christopher John Fields
• [Bioperl-guts-l] [16083] bioperl-live/trunk: [bug 2843]   Christopher John Fields
• [Bioperl-guts-l] [16084] bioperl-live/trunk/Changes: updates for bug numbers   Christopher John Fields
• [Bioperl-guts-l] [16085] bioperl-live/trunk/Changes: small date change, make this for the alpha   Christopher John Fields
• [Bioperl-guts-l] [16086] bioperl-live/trunk/Bio/SeqIO/fastq.pm: Peter's patch   Christopher John Fields
• [Bioperl-guts-l] [16087] bioperl-live/trunk/Bio/DB/SeqFeature.pm: trivial doc patch   Robert Buels
• [Bioperl-guts-l] [16088] bioperl-live/trunk/Bio/SeqFeature/Generic.pm: added more proper deprecation message for bp 1.7 to Bio::SeqFeature:: Generic::slurp_gff_file   Robert Buels
• [Bioperl-guts-l] [16089] bioperl-live/branches/branch-1-6: sync with trunk to r15684   Christopher John Fields
• [Bioperl-guts-l] [16090] bioperl-live/branches/branch-1-6: sync with trunk (to r15946)   Christopher John Fields
• [Bioperl-guts-l] [16091] bioperl-live/branches/branch-1-6: sync with main trunk completely ( a few tests failing)   Christopher John Fields
• [Bioperl-guts-l] [16092] bioperl-live/trunk: fix mask_columns, move tests over to SimpleAlign.t ( these probably will be split out again at a later point once SimpleAlign is cleaned up )   Christopher John Fields
• [Bioperl-guts-l] [16093] bioperl-live/trunk/t: move bugzilla tests to relevant test files, data to t/data, and remove   Christopher John Fields
• [Bioperl-guts-l] [16094] bioperl-live/trunk/Changes: add alpha designation   Christopher John Fields
• [Bioperl-guts-l] [16095] branches/gff_refactor/bioperl-live/trunk/.gitignore: added . gitignore for use when developing with git-svn   Robert Buels
• [Bioperl-guts-l] [16096] branches/gff_refactor/bioperl-live/trunk/Bio/SeqFeature/ TypedSeqFeatureI.pm: updated Bio::SeqFeature:: TypedSeqFeatureI to specify type_term() and source_term() methods, as well as alias the old ontology_term() to type_term()   Robert Buels
• [Bioperl-guts-l] [16097] branches/gff_refactor/bioperl-live/trunk/Bio/SeqFeature/ TypedSeqFeatureI.pm: added deprecation message to ontology_term() method in TypedSeqFeatureI   Chris Fields
• [Bioperl-guts-l] [16097] branches/gff_refactor/bioperl-live/trunk/Bio/SeqFeature/ TypedSeqFeatureI.pm: added deprecation message to ontology_term() method in TypedSeqFeatureI   Robert Buels
• [Bioperl-guts-l] [16097] branches/gff_refactor/bioperl-live/trunk/Bio/SeqFeature/ TypedSeqFeatureI.pm: added deprecation message to ontology_term() method in TypedSeqFeatureI   Robert Buels
• [Bioperl-guts-l] [16098] branches/gff_refactor: added distribution skeleton for Bio:: SeqFeature::Typed   Robert Buels
• [Bioperl-guts-l] [16099] branches/gff_refactor/Bio-FeatureIO/.gitignore: added gitignore file to Bio-FeatureIO distribution   Robert Buels
• [Bioperl-guts-l] [16100] branches/gff_refactor/bioperl-live/trunk/.gitignore: added TAGS to bioperl-live gitignore   Robert Buels
• [Bioperl-guts-l] [16101] branches/gff_refactor/Bio-SeqFeature-Typed: intermediate work on SF ::T   Robert Buels
• [Bioperl-guts-l] [16102] branches/gff_refactor/Bio-SeqFeature-Typed/Build.PL: added some Bio ::* module dependencies to Bio-SeqFeature-Typed dist   Robert Buels
• [Bioperl-guts-l] [16103] bioperl-live/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16104] bioperl-live/branches/branch-1-6/Bio/Root: bump to alpha 1   Christopher John Fields
• [Bioperl-guts-l] [16105] bioperl-live/trunk/maintenance/pod.pl: simplify script   Christopher John Fields
• [Bioperl-guts-l] [16106] bioperl-live/trunk/t/RemoteDB/HIV: changes re: warnings   Mark Allen Jensen
• [Bioperl-guts-l] [16107] bioperl-live/trunk/Bio/DB/Query/HIVQuery.pm: patch to track new return format @ LANL   Mark Allen Jensen
• [Bioperl-guts-l] [16108] bioperl-live/trunk/Bio: [cage cleaning]   Christopher John Fields
• [Bioperl-guts-l] [16109] bioperl-live/trunk/Bio: [cage cleaning]   Christopher John Fields
• [Bioperl-guts-l] [16110] bioperl-live/trunk: [cage cleaning]   Christopher John Fields
• [Bioperl-guts-l] [16111] bioperl-live/trunk/Bio: [cage cleaning]   Christopher John Fields
• [Bioperl-guts-l] [16112] bioperl-dev/trunk/ide/emacs/bioperl-mode/README: add README   Mark Allen Jensen
• [Bioperl-guts-l] [16113] bioperl-dev/tags/bioperl-mode-port-to-core-091609/: snapshot at port to core for 1.6.1 inclusion   Mark Allen Jensen
• [Bioperl-guts-l] [16114] bioperl-live/trunk: subdir for IDE support   Mark Allen Jensen
• [Bioperl-guts-l] [16115] bioperl-live/trunk/ide/bioperl-mode/site-lisp/: port to core   Mark Allen Jensen
• [Bioperl-guts-l] [16116] bioperl-live/trunk/ide/bioperl-mode/etc/: port to core   Mark Allen Jensen
• [Bioperl-guts-l] [16117] bioperl-live/trunk/ide/bioperl-mode/dist/: port to core   Mark Allen Jensen
• [Bioperl-guts-l] [16118] bioperl-live/trunk/ide/bioperl-mode/README: readme   Mark Allen Jensen
• [Bioperl-guts-l] [16119] bioperl-live/trunk: [cage cleaning]   Christopher John Fields
• [Bioperl-guts-l] [16120] bioperl-live/trunk/Bio: [cage cleaning]   Christopher John Fields
• [Bioperl-guts-l] [16121] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Fixed bug preventing the correct determination of a cross-contig spectrum   Florent E Angly
• [Bioperl-guts-l] [16122] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm:   Florent E Angly
• [Bioperl-guts-l] [16124] bioperl-live/tags/bioperl-1-6-0_001/: * tag 1.6.0_1 (1.6. 1 first alpha)   Mark A. Jensen
• [Bioperl-guts-l] [16124] bioperl-live/tags/bioperl-1-6-0_001/: * tag 1.6.0_1 (1.6. 1 first alpha)   Chris Fields
• [Bioperl-guts-l] [16124] bioperl-live/tags/bioperl-1-6-0_001/: * tag 1.6.0_1 (1.6. 1 first alpha)   Christopher John Fields
• [Bioperl-guts-l] [16125] bioperl-run/trunk/lib/Bio/Tools/Run/TigrAssembler.pm: Mostly cleanup   Florent E Angly
• [Bioperl-guts-l] [16126] bioperl-live/trunk/Bio/Root/Build.pm: [bug 2859]   Christopher John Fields
• [Bioperl-guts-l] [16127] bioperl-live/trunk/Changes: stub for 2nd alpha and small updates for last commit, doc and link fixes   Christopher John Fields
• [Bioperl-guts-l] [16128] bioperl-live/branches/branch-1-6: sync w/ main trunk, bump alpha version   Christopher John Fields
• [Bioperl-guts-l] [16129] bioperl-live/trunk/Bio/DB/GenBank.pm: document the issues with get_Seq_by_acc/version per mail list ( hartzell and bill)   Christopher John Fields
• [Bioperl-guts-l] [16130] bioperl-live/trunk: added tests for Bio::DB::SeqFeature:: Store using SQLite adaptor   Lincoln Stein
• [Bioperl-guts-l] [16131] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/Pg.pm: removing the postgres adaptor' s attempts to create a temp database for tests, as it   Scott Cain
• [Bioperl-guts-l] [16132] bioperl-live/trunk/ide/bioperl-mode/site-lisp/bioperl-mode.el: fix source viewer for method view   Mark Allen Jensen
• [Bioperl-guts-l] [16133] bioperl-live/trunk/ide/bioperl-mode/dist: retarred (r16132)   Mark Allen Jensen
• [Bioperl-guts-l] [16134] bioperl-live/trunk/t/SeqTools/Backtranslate.t: * use_ok, not ' use ok' (courtesy of Bruno Vecchi)   Christopher John Fields
• [Bioperl-guts-l] [16135] bioperl-live/trunk/t/SeqIO/raw.t: do not use 'use' when late loading as 'use' loads at compile time (using 'test_skip' loads them dynamically)   Christopher John Fields
• [Bioperl-guts-l] [16136] bioperl-live/trunk/t/SeqIO/raw.t: * Algorithm::Diff needs imports, using use_ok for that one   Christopher John Fields
• [Bioperl-guts-l] [16137] bioperl-live/trunk: * load module dynamically instead of requiring it up-front ( seems to pass everything fine)   Christopher John Fields
• [Bioperl-guts-l] [16138] bioperl-live/trunk/t/SeqIO/raw.t: bump test_skip number   Christopher John Fields
• [Bioperl-guts-l] [16139] bioperl-live/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16140] bioperl-live/trunk/scripts: add einfo script   Christopher John Fields
• [Bioperl-guts-l] [16141] bioperl-live/trunk/Bio/Root/IO.pm: use LWP:: UserAgent rather than LWP::Simple   Mark Allen Jensen
• [Bioperl-guts-l] [16142] bioperl-live/trunk: fix POD multiple linkage issues   Christopher John Fields
• [Bioperl-guts-l] [16143] bioperl-live/trunk/Bio/DB/HIV/HIVQueryHelper.pm: silence multiple linkage warnings (Mark, you might want to check these)   Christopher John Fields
• [Bioperl-guts-l] [16144] bioperl-live/trunk/t: move gmap tests to SearchIO   Christopher John Fields
• [Bioperl-guts-l] [16145] bioperl-live/trunk: * remove the SQLite test ( this is autogenerated from Build.PL)   Christopher John Fields
• [Bioperl-guts-l] [16146] bioperl-live/trunk/t/PodSyntax.t: Only test specific directories; specifying '.' redundantly runs tests on modules copied to blib   Christopher John Fields
• [Bioperl-guts-l] [16147] bioperl-live/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16148] bioperl-live/tags/bioperl-1-6-0_002/: tag next alpha   Christopher John Fields
• [Bioperl-guts-l] [16149] bioperl-live/branches/branch-1-6/t/LocalDB/SeqFeature_SQLite.t: remove from branch   Christopher John Fields
• [Bioperl-guts-l] [16150] bioperl-live/trunk/ide/bioperl-mode/site-lisp: xemacs compatibility and distribution tar   Mark Allen Jensen
• [Bioperl-guts-l] [16151] bioperl-live/branches/branch-1-6/t: merge over test fixes missed in previous merge (found by svn diff)   Christopher John Fields
• [Bioperl-guts-l] [16152] bioperl-live/trunk/Build.PL: cmake sure SQLite test is named correctly via dsn, and delete upon cleanup   Christopher John Fields
• [Bioperl-guts-l] [16153] bioperl-live/branches/branch-1-6: sync with main trunk, bump version to alpha 3   Christopher John Fields
• [Bioperl-guts-l] [16154] bioperl-live/trunk/BUGS: update to remove a couple of fixed ones ( we should probably remove this file at some point; makes more sense to point to the bugzilla/RT queues)   Christopher John Fields
• [Bioperl-guts-l] [16155] bioperl-live/branches/branch-1-6/BUGS: sync that last bit   Christopher John Fields
• [Bioperl-guts-l] [16156] bioperl-live/tags/bioperl-1-6-0_003/: tag next alpha ( fingers crossed)   Christopher John Fields
• [Bioperl-guts-l] [16157] bioperl-db/trunk/Build.PL: main trunk version is wrong   Christopher John Fields
• [Bioperl-guts-l] [16158] bioperl-live/trunk/Bio/Matrix/IO/phylip.pm: comma!   Mark Allen Jensen
• [Bioperl-guts-l] [16159] bioperl-live/trunk/Bio/Index/Fasta.pm: [bug 2917]   Christopher John Fields
• [Bioperl-guts-l] [16160] bioperl-live/trunk/t/SeqIO/asciitree.t: fix asciitree TODO for IRIX   Christopher John Fields
• [Bioperl-guts-l] [16161] bioperl-live/trunk/t/SeqIO/asciitree.t: slightly better test failure   Christopher John Fields
• [Bioperl-guts-l] [16162] bioperl-live/trunk/t/Root/Utilities.t: wrong number of skipped tests (fails unless gzip is installed, e.g Win)   Christopher John Fields
• [Bioperl-guts-l] [16163] bioperl-live/branches/anydbm-branch/: for generalizing the use of DB_File to AnyDBM_File   Mark Allen Jensen
• [Bioperl-guts-l] [16164] bioperl-live/trunk/Bio/SeqIO/scf.pm: fix binmode issue with scf on Windows ( thx to maj for pointing out the problem)   Christopher John Fields
• [Bioperl-guts-l] [16165] bioperl-live/trunk/BioPerl.pod: add back bioperl.pod as BioPerl. pod (for proper CPAN descriptions for distributions)   Christopher John Fields
• [Bioperl-guts-l] [16166] bioperl-live/trunk/Changes: update Changes   Christopher John Fields
• [Bioperl-guts-l] [16167] bioperl-live/trunk/Bio: minor doc updates   Christopher John Fields
• [Bioperl-guts-l] [16168] bioperl-live/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16169] bioperl-live/branches/branch-1-6/Bio/Root: bump alpha   Christopher John Fields
• [Bioperl-guts-l] [16170] bioperl-live/tags/bioperl-1-6-0_003/branch-1-6/: tag fourth ( and hopefully last) alpha   Christopher John Fields
• [Bioperl-guts-l] [16171] bioperl-live/tags/bioperl-1-6-0_004/: retag   Christopher John Fields
• [Bioperl-guts-l] [16172] bioperl-live/tags/bioperl-1-6-0_003/branch-1-6/: remove odd miscommit from tag   Christopher John Fields
• [Bioperl-guts-l] [16173] bioperl-live/branches/anydbm-branch/Bio/DB/Flat/BinarySearch.pm: a synopsis for edification and enjoyment   Mark Allen Jensen
• [Bioperl-guts-l] [16174] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: A minimal DBM for tying hashes to SQLite   Mark Allen Jensen
• [Bioperl-guts-l] [16175] bioperl-live/branches/anydbm-branch/Bio/DB/Qual.pm: adding Bio::DB: :SQLite_File to   Mark Allen Jensen
• [Bioperl-guts-l] [16176] bioperl-live/branches/anydbm-branch/Bio/DB/FileCache.pm: Allowing FileCache to use AnyDBM_File   Mark Allen Jensen
• [Bioperl-guts-l] [16177] bioperl-live/branches/anydbm-branch/t/LocalDB/SQLite_File.t: tests for Bio::DB::SQLite_File   Mark Allen Jensen
• [Bioperl-guts-l] [16178] bioperl-live/branches/anydbm-branch/t/LocalDB/Index.t: weakens the DB_File requirement   Mark Allen Jensen
• [Bioperl-guts-l] [16179] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: verbs, schmerbs.   Mark Allen Jensen
• [Bioperl-guts-l] [16180] bioperl-live/trunk: * move BioPerl.pod -> BioPerl.pm (PBP)   Christopher John Fields
• [Bioperl-guts-l] [16181] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: attempting better emulation of DB_File   Mark Allen Jensen
• [Bioperl-guts-l] [16182] bioperl-live/trunk/Bio/Root/Build.pm: remove hard-path shebang   Christopher John Fields
• [Bioperl-guts-l] [16183] bioperl-live/trunk/Bio/SeqIO/tinyseq.pm: [RT 50048]   Christopher John Fields
• [Bioperl-guts-l] [16184] bioperl-live/trunk/BioPerl.pm: update for this version   Christopher John Fields
• [Bioperl-guts-l] [16185] bioperl-live/trunk/Changes: Note changes   Christopher John Fields
• [Bioperl-guts-l] [16186] bioperl-live/branches/branch-1-6: * merge changes from main trunk   Christopher John Fields
• [Bioperl-guts-l] [16187] bioperl-live/tags/bioperl-1-6-0_005/: final alpha   Christopher John Fields
• [Bioperl-guts-l] [16188] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: slowing morphing into DB_File   Mark Allen Jensen
• [Bioperl-guts-l] [16189] bioperl-live/trunk/t/LocalDB: tests do not require both DB_File and BerekelyDB, was masking a significant bug   Christopher John Fields
• [Bioperl-guts-l] [16190] bioperl-live/trunk/Bio/DB/Flat/BDB/fasta.pm: Fix ODBA bug related to recent changes for FASTA seq validation ( masked in past alpha releases)   Christopher John Fields
• [Bioperl-guts-l] [16191] bioperl-live/branches/branch-1-6: bump alpha to test ODBA-related bug fix   Christopher John Fields
• [Bioperl-guts-l] [16192] bioperl-live/tags/bioperl-1-6-0_006/: final final alpha?!?   Christopher John Fields
• [Bioperl-guts-l] [16193] bioperl-live/trunk: Initital deposition of Align/Graphics. pm and its test script   Weigang Qiu
• [Bioperl-guts-l] [16194] bioperl-live/trunk/Changes: add last changes, including 1.6. 1 point release info   Mark A. Jensen
• [Bioperl-guts-l] [16194] bioperl-live/trunk/Changes: add last changes, including 1.6. 1 point release info   Chris Fields
• [Bioperl-guts-l] [16194] bioperl-live/trunk/Changes: add last changes, including 1.6. 1 point release info   Christopher John Fields
• [Bioperl-guts-l] [16195] bioperl-live/trunk/Changes: typo   Christopher John Fields
• [Bioperl-guts-l] [16196] bioperl-live/trunk: more doc updates   Christopher John Fields
• [Bioperl-guts-l] [16197] bioperl-live/branches/branch-1-6: * bump point version   Christopher John Fields
• [Bioperl-guts-l] [16198] bioperl-live/tags/bioperl-release-1-6-1/: tag 1.6.1 point release   Christopher John Fields
• [Bioperl-guts-l] [16199] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: hey, why NOT emulate DB_File?   Mark Allen Jensen
• [Bioperl-guts-l] [16200] bioperl-live/branches/anydbm-branch/t/LocalDB: tests tests tests   Mark Allen Jensen
• [Bioperl-guts-l] [16201] bioperl-db/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16202] bioperl-network/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16203] bioperl-run/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16204] bioperl-network/branches/branch-1-6/t: merge over tests ( these were missed but caught with global diff)   Christopher John Fields
• [Bioperl-guts-l] [16205] bioperl-db/trunk: some pod cleaning   Christopher John Fields
• [Bioperl-guts-l] [16206] bioperl-db/trunk/lib/Bio/DB/EasyArgv.pm: fix empty POD section   Christopher John Fields
• [Bioperl-guts-l] [16207] bioperl-network/trunk: * POD cleanup   Christopher John Fields
• [Bioperl-guts-l] [16208] bioperl-run/trunk/lib/Bio: * pod fixes   Christopher John Fields
• [Bioperl-guts-l] [16209] bioperl-run/trunk/t/Infernal.t: skip tests if infernal isn' t installed   Christopher John Fields
• [Bioperl-guts-l] [16210] bioperl-live/branches/anydbm-branch: very close: BDB interface to both   Mark Allen Jensen
• [Bioperl-guts-l] [16211] bioperl-run/trunk/t/data/purine.added.fa: add test data for cmalign   Christopher John Fields
• [Bioperl-guts-l] [16212] bioperl-run/trunk/t/gmap-run.t: skip tests if executable isn' t installed   Christopher John Fields
• [Bioperl-guts-l] [16213] bioperl-run/trunk/Changes: update changes   Christopher John Fields
• [Bioperl-guts-l] [16214] bioperl-db/trunk/Changes: update Changes   Christopher John Fields
• [Bioperl-guts-l] [16215] bioperl-network/trunk/Changes: update changes   Christopher John Fields
• [Bioperl-guts-l] [16216] bioperl-db/branches/branch-1-6: sync with main trunk   Christopher John Fields
• [Bioperl-guts-l] [16217] bioperl-db/tags/db-1-6-0_001/: tag db 1.6.0 alpha 1   Christopher John Fields
• [Bioperl-guts-l] [16218] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI: fixed bug which caused an INSERT statement to be erroneously called whenver searching for a seq_id that does not exist   Lincoln Stein
• [Bioperl-guts-l] [16219] bioperl-network/branches/branch-1-6: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [16220] bioperl-network/tags/network-1-6-0_001/: tag network 1.6.0 alpha 1   Christopher John Fields
• [Bioperl-guts-l] [16221] bioperl-run/branches/branch-1-6: sync with trunk   Christopher John Fields
• [Bioperl-guts-l] [16222] bioperl-run/tags/run-1-6-1_001/: tag run 1.6.1 alpha 1 ( note that bp-run is one point release ahead of the others)   Christopher John Fields
• [Bioperl-guts-l] [16223] bioperl-live/branches/anydbm-branch/Bio/DB/AnyDBMImporter.pm: solving the import problem   Mark Allen Jensen
• [Bioperl-guts-l] [16224] bioperl-db/trunk/MANIFEST.SKIP: remove MANIFEST.SKIP   Christopher John Fields
• [Bioperl-guts-l] [16225] bioperl-db/branches/branch-1-6/MANIFEST.SKIP: remove MANIFEST.SKIP   Christopher John Fields
• [Bioperl-guts-l] [16226] bioperl-db/tags/db-1-6-0_001/MANIFEST.SKIP: removing MANIFEST.SKIP (yes, I know, changing a tag is bad, yada yada yada)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2810] SeqUtils not copying SeqFeature tags - part 2 - revcom this time   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2861] blastxml and bsml_sax tests try to access internet even when network tests are skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2861] blastxml and bsml_sax tests try to access internet even when network tests are skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2861] blastxml and bsml_sax tests try to access internet even when network tests are skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2861] blastxml and bsml_sax tests try to access internet even when network tests are skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2881] An .scf file written from a Bio::Seq::Quality object cannot be read again   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2908] ecoli.nt not available from ftp://ncbi.nlm.nih.gov, causes t/Tools/Run/StandaloneBlast.t to fail   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2908] New: ecoli.nt not available from ftp://ncbi.nlm.nih.gov, causes t/Tools/Run/StandaloneBlast.t to fail   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2909] it is better to update the Bio::Tools::RepeatMasker module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2909] it is better to update the Bio::Tools::RepeatMasker module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2909] New: it is better to update the Bio::Tools::RepeatMasker module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2911] New: SimpleAlign select doc inconstistency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2911] SimpleAlign select doc inconstistency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2912] New: Some of the scripts linked here are not found   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2913] New: Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2914] ftp package no longer available during BioPerl1.6 installation   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2914] New: ftp package no longer available during BioPerl1.6 installation   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2915] Infinite loop of "_write_line_GenBank_regex" under certain conditions   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2915] New: Infinite loop of "_write_line_GenBank_regex" under certain conditions   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2917] Fasta validation error in Bio::SeqIO::fasta thrown when used with Bio::Index::Fasta on Windows   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2917] Fasta validation error in Bio::SeqIO::fasta thrown when used with Bio::Index::Fasta on Windows   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2917] Fasta validation error in Bio::SeqIO::fasta thrown when used with Bio::Index::Fasta on Windows   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2917] Fasta validation error in Bio::SeqIO::fasta thrown when used with Bio::Index::Fasta on Windows   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2917] New: Fasta validation error in Bio::SeqIO::fasta thrown when used with Bio::Index::Fasta on Windows   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2920] New: Problem with ClustalW 1.83 profile_align function   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2920] Problem with ClustalW 1.83 profile_align function   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2920] Problem with ClustalW 1.83 profile_align function   bugzilla-daemon at portal.open-bio.org

Last message date: Wed Sep 30 16:45:17 EDT 2009
Archived on: Wed Sep 30 16:45:20 EDT 2009

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