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BUGS
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BUGS
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# $Id: BUGS,v 1.7 2006-11-16 10:51:50 sendu Exp $
Known Bugs
Bugs are tracked at this URL:
https://redmine.open-bio.org/projects/bioperl/
Bioperl 1.6 series
=============
Though a stable release, some bugs and enhancements remain for this series
that will be addressed in future point releases. For a full list please see:
https://redmine.open-bio.org/projects/bioperl/
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);