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BUGS
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BUGS
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# $Id: BUGS,v 1.4 2002-12-31 13:09:05 birney Exp $
Known Bugs
Bioperl 1.2
===========
* The searchio.t test is failing on cygwin installations (and
nowhere else). We need a developer who works with cygwin to
help us out here. We suspect something to do with temporary file
opening.
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);