[Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4

Chris Fields cjfields at illinois.edu
Wed Jan 21 23:39:15 EST 2009


I would like to announce that the fourth release candidate for BioPerl  
1.6 is now available for testing.  This RC was necessary in order to  
fix several tests with Windows ActivePerl.  Barring any problems this  
should represent the final release and should be tagged as such this  

A quick (and hopefully final) note on versioning: due to issues with  
alpha numbered versions on CPAN possibly overwriting or taking  
precedence over a stable release, this release candidate has a VERSION  
of 1.005009_004 (or 1.005009004).  This will be switched to 1.006000  
(no alpha) once the release is final.

The RC has been uploaded to CPAN and should be available soon under  
authorname CJFIELDS.  It can also be found here:


In the meantime, the release candidates can be directly downloaded here:


Signature file:

Again, just to note we will be releasing bioperl-run, bioperl-db,  
bioperl-network, and others separately once the final 1.6 release is  
complete.  These will likely go through a (much more abbreviated)  
release candidate cycle depending on any problems that arise.

Please feel free to report issues with testing, installation, etc. on  
the mail list and on this page:


Since the last release:

1) A preliminary ActiveState PPM is available and is located in the  
BioPerl Release Candidate repository (the directions for installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) 
.  However, a few 'required' PPM modules are not currently available  
for perl 5.10, particularly GraphViz and XML-SAX-Writer.  We will  
attempt adding the necessary PPMs to the BioPerl PPM directory soon.   
In the meantime, we can specifically remove those requirements for  
BioPerl PPM installation if no one objects; the modules affected would  
be Bio::SeqIO::tigrxml (XML-SAX-Writer) and  
Bio::PhyloNetwork::GraphViz (GraphViz).

2) Several failures for tests have been corrected.  If any additional  
system-dependent failures occur they will be fixed in a 1.6 point  
release at a later time.

3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the 1.6.0  
release due to failing tests but may appear in a future 1.6 release  
once the code stabilizes.



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