[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Chris Fields cjfields at illinois.edu
Fri Jan 16 19:11:13 UTC 2009


I would like to announce that the third (and hopefully final) release  
candidate for BioPerl 1.6 is now available for testing.  As this is  
likely the final release candidate, any errors encountered during  
regression tests would be greatly appreciated.

A quick 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_003 (or  
1.005009003).  This will be switched to 1.006000 (no alpha) once the  
release is final.

The RC is currently being uploaded to CPAN and should be available in  
the next 24-48 hours under authorname CJFIELDS.  In the meantime, the  
release candidates can be directly downloaded here:


Signature file:

A preliminary ActiveState PPM is also available and is located in the  
BioPerl Release Candidate repository; the directions for installation  
are here:


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


Again, just to note we will be releasing bioperl-run, bioperl-db,  
bioperl-network, and others separately once the final 1.6 release is  

Since the last release:


1) Remote database tests are now a bit more robust.
2) Bio::DB::GDB and related tests have been deprecated and removed  
(GDB is no longer available).
3) More warnings and test failures (via CPAN Testers) now fixed.
4) BLAST-related file and parsing issues resolved (per Scott Markel).
5) Small test fixes.

Known Issues:

1) Warnings for Bio::Assembly tests are for incomplete phrap parsing.   
These modules will be a focus of BioPerl 1.7; in the meantime I'll see  
about quenching the tests.
2) Warnings for Bio::Annotation tests can be fixed by an upgrade to  
the latest Data::Stag (this is NOT a required upgrade).
3) PPM issues; note this is not high on our priority list ATM but I  
will try to address it for the next release.
4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with  


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