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cjfields
cjfields committed Sep 25, 2009
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-=head1 PRIMARY AUTHORS AND MAJOR CONTRIBUTORS TO BIOPERL
-
-=head2 Releases co-ordinated and submitted by bioperl core devs.
-
-=over
-
-=item * Sendu Bala <bix at sendu.me.uk>
-
-=item * Chris Dagdigian <dag at sonsorol.org>
-
-=item * Christopher Fields <cjfields at bioperl.org>
-
-=item * Mark Jensen <maj@fortinbras.us>
-
-=item * Hilmar Lapp <hlapp at gmx.net>
-
-=item * Heikki Lehv�slaiho <heikki at ebi.ac.uk>
-
-=item * Aaron Mackey <amackey at pcbi.upenn.edu>
-
-=item * Brian Osborne <bosborne at bioteam.net>
-
-=item * Jason Stajich <jason at bioperl.org>
-
-=item * Lincoln Stein <lstein at cshl.org>
-
-=back
-
-=head2 Previous Bioperl Coordinators:
-
-=over
-
-=item * Ewan Birney <birney at ebi.ac.uk>
-
-=item * Steven Brenner <brenner at compbio.berkeley.edu>
-
-=item * Georg Fuellen <fuellen at alum.mit.edu>
-
-=item * Steve Chervitz <sac at bioperl.org>
-
-=back
-
-=head2 Major Contributors
-
-(Feel free to add descriptions of which modules you are responsible
-for if you see fit)
-
-=over
-
-=item * Richard Adams <Richard.Adams at ed.ac.uk>
-
-=item * Shuly Avraham <avraham at cshl.org> - Bio::Graphics::Glyph
-
-=item * Peter Blaiklock <pblaiklo at restrictionmapper.org>
-
-=item * Benjamin Berman <benb at fruitfly.berkeley.edu>
-
-=item * Matthew Betts <Matthew.Betts at ii.uib.no>
-
-=item * David Block <dblock at gnf.org>
-
-=item * Kris Boulez <kris.boulez at algonomics.com>
-
-=item * Tim Bunce <Tim.Bunce at pobox.com> - code optimizations
-
-=item * Scott Cain <scott at scottcain.net> - Bio::Graphics::Glyph, Bio::DB::GFF::Adaptor::dbi::pg, GFF related tools and scripts
-
-=item * Yee Man Chan <ymc at yahoo.com> - Bio::Tools::dpAlign
-
-=item * Brad Chapman <chapmanb at arches.uga.edu>
-
-=item * Roy R. Chaudhuri <roy.chaudhuri at gmail.com> - Bio::SeqUtils Bio::Align::Utilities
-
-=item * Michele Clamp <michele at sanger.ac.uk>
-
-=item * Malcolm Cook <mec at stowers-institute.org>
-
-=item * Tony Cox <avc at sanger.ac.uk>
-
-=item * James Cuff <james at sanger.ac.uk>
-
-=item * Andrew Dalke <dalke at acm.org>
-
-=item * Allen Day <allenday at ucla.edu>
-
-=item * Jared Fox <jaredfox at ucla.edu> - Bio::SeqIO::interpro
-
-=item * Brian O'Connor <boconnor at ucla.edu> - Bio::TreeIO::svggraph
-
-=item * James Diggans <JDiggans at genelogic.com>
-
-=item * Peter Dimitrov <dimitrov at gnf.org> - Bio::Ontology
-
-=item * Rich Dobson <r.j.dobson at qmul.ac.uk> - Bio::PopGen::IO::hapmap,phase
-
-=item * Paul Edlefsen <pedlefsen at systemsbiology.org>
-
-=item * Rob Edwards <redwards at utmem.edu> - Bio::Restriction
-
-=item * Arne Elofsson <arne at sbc.su.se>
-
-=item * David Evans <David.Evans at vir.gla.ac.uk>
-
-=item * Mark Fiers <M.W.E.J.Fiers at plant.wag-ur.nl>
-
-=item * The Fugu Team <fuguteam at fugu-sg.org>
-
-=item * Luc Gauthier <lgauthie at hotmail.com>
-
-=item * James Gilbert <jgrg at sanger.ac.uk>
-
-=item * Nat Goodman
-
-=item * Ed Green <ed at compbio.berkeley.edu>
-
-=item * Matthew Hahn <matthew.hahn at duke.edu>
-
-=item * Roger Hall <roger at iosea.com>
-
-=item * Todd Harris <harris at cshl.org> - SVG support in Bio::Graphics
-
-=item * Mauricio Herrera Cuadra <mauricio at open-bio.org>
-
-=item * Ian Holmes <ihn at fruitfly.org>
-
-=item * Shawn Hoon <shawnh at fugu-sg.org>
-
-=item * Robert Hubley <rhubley at systemsbiology.org>
-
-=item * Joseph Insana <insana at ebi.ac.uk> - Bio::LiveSeq
-
-=item * Donald Jackson <donald.jackson at bms.com> - SiRNA
-
-=item * Keith James <kdj at sanger.ac.uk> - Bio::Tools::Geneid
-
-=item * Mark A. Jensen <maj at fortinbras.us> - Bio::DB::HIVQuery, Bio::Search::Tiling
-
-=item * Nicolas Joly <njoly at pasteur.fr>
-
-=item * Ian Korf <ikorf at sapiens.wustl.edu>
-
-=item * Dan Kortschak <kortschak at rsbs.anu.edu.au>
-
-=item * Arek Kasprzyk <arek at ebi.ac.uk>
-
-=item * Andreas K�h�ri <andreas.kahari at ebi.ac.uk>
-
-=item * Charles C. Kim <cckim at stanford.edu>
-
-=item * Stefan Kirov <skirov at utk.edu> - Bio::Matrix::PSM
-
-=item * Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
-
-=item * Josh Lauricha <laurichj at cs.ucr.edu> - Bio::SeqIO::tigr
-
-=item * Eckhard Lehmann <ecky at e-lehmann.de>
-
-=item * Catherine Letondal <letondal at pasteur.fr>
-
-=item * Philip Lijnzaad <p.lijnzaad at med.uu.nl>
-
-=item * Brad Marshall <bradmars at yahoo.com>
-
-=item * Chad Matsalla <chad at dieselwurks.com>
-
-=item * Andrew Macgregor <andrew at anatomy.otago.ac.nz>
-
-=item * Sheldon McKay <mckays at cshl.edu>
-
-=item * Dave Messina <dmessina at cpan.org> - Deobfuscator, judicious meddling
-
-=item * Chase Miller <chmille4 at gmail.com> - Bio::Nexml and related IO modules
-
-=item * Juha Muilu <muilu at ebi.ac.uk>
-
-=item * Chris Mungall <cjm at fruitfly.org>
-
-=item * Giri Narasimhan <giri at cs.fiu.edu>
-
-=item * Xiaokang Pan <pan at cshl.org> - Bio::Graphics::Glyph
-
-=item * Jong Park
-
-=item * Matthew Pocock <matthew_pocock at yahoo.co.uk>
-
-=item * Lorenz Pollack <lorenz at ist.org> -- BPlite porting
-
-=item * Richard Resnick -- original Bio::Seq
-
-=item * Todd Richmond <todd at andrew2.stanford.edu>
-
-=item * Peter Schattner <schattner at alum.mit.edu>
-
-=item * Torsten Seemann <torsten.seemann at infotech.monash.edu.au> -- Bio::Tools::Run::StandaloneBlast
-
-=item * Martin Senger <senger at ebi.ac.uk> -- Bio::Biblio
-
-=item * Nigam Shah <nigam at psu.edu>
-
-=item * Shengqiang Shu <sshu at bdgp.lbl.gov> - Bio::Graphics::Glyph
-
-=item * Allen Smith <allens at cpan.org> -- Bio::Matrix and Bio::SimpleAlign fixes
-
-=item * Marc Sohrmann <ms2 at sanger.ac.uk>
-
-=item * Robson Francisco de Souza <robfsouza at gmail.com> - Bio::Assembly
-
-=item * Mark Southern <mark_southern at merck.com>
-
-=item * Will Spooner <whs at sanger.ac.uk>
-
-=item * Arne Stabenau <stabenau at ebi.ac.uk>
-
-=item * Elia Stupka <elia at fugu-sg.org>
-
-=item * Gert Thijs <gert.thijs at esat.kuleuven.ac.be>
-
-=item * James Thompson <tex at biosysadmin.com> - Bio::Matrix::PSM protein-related modules.
-
-=item * Charles Tilford <tilfordc at bms.com>
-
-=item * Anthony Underwood <aunderwood at phls.org.uk>
-
-=item * Paul-Christophe Varoutas
-
-=item * Andrew G. Walsh <paeruginosa at hotmail.com>
-
-=item * Kai Wang <tumorimmunology at yahoo.com>
-
-=item * Gary Williams <G.Williams at hgmp.mrc.ac.uk>
-
-=item * Mark Wilkinson <mwilkinson at gene.pbi.nrc.ca>
-
-=item * Helge Weissig <helgew at sdsc.edu>
-
-=item * Juguang Xiao <juguang at tll.org.sg>
-
-=item * Alex Zelensky <alex_zelensky at mac.com> - Bioperl-DB
-
-=item * Peili Zhang <peili at morgan.harvard.edu>
-
-=item * Christian M. Zmasek <czmasek at gnf.org> - Bio::Phenotype & Bio::Ontology
-
-=back
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@@ -1,141 +0,0 @@
-# $Id: BUGS,v 1.7 2006-11-16 10:51:50 sendu Exp $
-
-Known Bugs
-
-Bugs are tracked at this URL:
-http://bugzilla.bioperl.org/
-
-Bioperl 1.6.0
-=============
-
-Though a stable release, a few bugs and enhancements remain for this series
-that will be addressed in future point releases:
-
-Bug Summary (additional info)
-
-2247 Have Bio::SearchIO::blast methods available for other BLAST parsers
- (enhancement request)
-2332 Software for analysis of redundant fragments of affys human mitochip v2
- (API hasn't stabilized, may appear in a 1.6 point release)
-2439 multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO
- (partially implemented)
-2463 bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface
- (enhancement request)
-2476 "Undefined sub-sequence" when processing tblastx output
- (related to HSP tiling)
-2482 paml4 mlc file fails to parse
- (may require refactoring Bio::Tools::Phylo::PAML)
-2492 Method "pi" in package Bio::PopGen::Statistics
- (awaiting comment from Jason)
-2513 creating a Bio::SeqFeature::Annotation object downloads the entire so.obo
- (should allow local copies)
-2594 Bio::Species memory leak
- (fix implemented, but additional leaks likely remain)
-2673 original fields not inherited by seq objects in alignment slices
- (request for bequest/bequeath behavior for attribute carryover)
-2686 WU-BLAST XML support
- (partially implemented, but issues remain)
-2691 Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency
- (related to bug 2332 above)
-2696 global verbosity does not propagate to new objects post-set
- (requires more specific implementation details)
-2700 Refactor Build.PL
- (some of the behind-the-scenes stuff is a little klunky)
-2702 Scripts recopied upon each call to './Build test'
- (minor bug)
-2703 Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP
- (minor bug that mistakes format)
-2707 Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in
- filenames, but Bio::SearchIO::blast does
- (bug within StandAloneBlast)
-2715 LocatableSeq symbols are globally set
- (bug related to sequence symbol issues; rarely surfaces but needs addressing)
-
-
-Bioperl 1.5.2
-=============
-
-There are no known installation bugs in 1.5.2 per se, but issues with
-external programs may cause problems. See the following URL for details:
-http://www.bioperl.org/wiki/Release_1.5.2#Notes
-
-
-Bioperl 1.2
-===========
-
- * The StandAloneBlast.t test is failing on cygwin installations (and
- nowhere else). We suspect something to do with temporary file
- opening. Fixed in 1.4 (set TMPDIR).
-
-
-Bioperl 0.9.0
-=============
-
- * Bio::Tools::Blast continues to cause problems for some people. As
- it is not actively maintained there are a slew of reported bugs for
- it that have not been fixed.
-
- * Bio::Tools::Run::Alignment::TCoffee - t_coffee binary does not get
- all parameters it needs when aligning (two) two DNA sequences
- (jitterbug #966).
-
- * Bio::Tools::Run::ClustalW and t/ClustalW will report errors for
- clustalw versions 1.8x due to a bug in clustalw.
-
- * Bio::DB::GenBank continues to have intermittent errors. Bio::DB::GDB
- is also unreliable at times and one can safely ignore errors from
- these during a make test.
- Bio::DB::GenBank is unable to download whole contig files as well
- as NCBI ref seqs like NT_* numbers unless the -format flag is
- passed in and specified as 'fasta' in the constructor.
- get_Stream_by_batch() also has intermittent errors which are being
- tracked down.
-
-
-Bioperl 0.7.2
-=============
-
- * NCBI has changed some of the cgi scripts for retrieving sequences
- online which as resulted in some of the DB methods from not working
- consistently. We are addressing these in the 0.9.x and 1.0 series
- of releases. We recommend using the Bio::DB::EMBL object that is
- part of the later releases.
-
- Additionally RefSeq Contigs are not properly downloaded, please see
- the bioperl list archives for information about potential
- workarounds and ongoing development effort to address these.
-
-
-Bioperl 0.7.1
-=============
-
- * Bio::Tools::BPlite does not parse and set frame properly for
- tblastx reports (Jitterbug bug # 978).
-
- * Bio::Tools::BPlite interface needs to be updated to fix parsing
- more than bl2seq report report (Jitterbug bug #940), this has been
- fixed on the main code trunk and will be part of the next major
- bioperl release.
-
- * If File::Temp is not installed, tempdirs are not cleaned up
- properly. This is fixed on main code trunk with the introduction
- of rmtree method in Bio::Root::IO, however, it is best to install
- File::Temp when running 0.7 branch code.
-
- * Bio::Tools::Blast does not allow users to run blast, instead use
- Bio::Tools::Run::StandAloneBlast to run local blasts. To submit
- jobs to a remote blast server like NCBI a module
- Bio::Tools::Run::RemoteBlast has been written but is part of the
- main trunk code and must be obtained through CVS until the next
- major bioperl release.
-
-
-Bioperl 0.7
-===========
-
- * Bio::Tools::BPlite doc error lists
- code synopsis code as
- my $parser = new BPlite(\*FH);
- should be
- my $parser = new Bio::Tools::BPlite(\*FH);
-
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