[Bioperl-announce-l] BioPerl 1.6 RC2 is now available

Chris Fields cjfields at illinois.edu
Wed Jan 7 18:57:14 UTC 2009


I would like to announce the second release candidate for BioPerl 1.6  
is available for testing.

A quick note on versioning: due to issues with alpha numbered versions  
on CPAN possibly overwriting a stable release, this release candidate  
has a VERSION of 1.005009_002 (or 1.005009002).  This will be switched  
to 1.006000 (no alpha) once the release is final.

RC2 has been uploaded to CPAN is available under authorname CJFIELDS.   
 From the CPAN shell:

cpan[1]> install CJFIELDS/BioPerl-1.5.9_2.tar.gz

RC2 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) Some cruft from testing the last release is no longer present.
2) Several warnings and test failures (via CPAN Testers) now fixed.

Known Issues:

1) A very recent change in ENSembl data causes one of the Map.t tests  
to fail; this has already been fixed and will be present in the next  
(final?) release.
2) Some odd warnings for Bio::Assembly tests are still present, but  
they are harmless.  Nevertheless they will be addressed prior to the  
next release.
3) Warnings for Bio::Annotation tests can be fixed by an upgrade to  
the latest Data::Stag (this is NOT a required upgrade).
4) PPM issues; note this is not high on our priority list ATM but I  
will try to address it for the next release).



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