[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Chris Fields cjfields at illinois.edu
Tue Jan 20 23:36:37 EST 2009


Scott,

I'll go ahead and take it out then.  We can add it back in later when  
everything's passing.

I'm planning on packaging RC4 (final RC) up tomorrow; ran into a few  
issues with Windows tests.  Barring additional problems the final 1.6  
release should be this weekend.

chris

On Jan 20, 2009, at 9:59 PM, Scott Cain wrote:

> Hi Chris,
>
> I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working
> by the release of 1.6, but it will have to wait for a point release at
> some time in the near future.  I can't get it to pass tests, so please
> remove it from the 1.6 release.
>
> Scott
>
>
> On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields  
> <cjfields at illinois.edu> wrote:
>> All,
>>
>> 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:
>>
>> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2
>> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz
>> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip
>>
>> Signature file:
>> http://bioperl.org/DIST/SIGNATURES.md5
>>
>> A preliminary ActiveState PPM is also available and is located in the
>> BioPerl Release Candidate repository; the directions for  
>> installation are
>> here:
>>
>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>>
>> Please feel free to report issues with testing, installation, etc.  
>> on the
>> mail list and on this page:
>>
>> http://www.bioperl.org/wiki/Release_1.6_Testing
>>
>> 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.
>>
>> Since the last release:
>>
>> Fixes:
>>
>> 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
>> SVG::Graph.
>>
>> Enjoy!
>>
>> chris
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>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
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