[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Scott Cain scott at scottcain.net
Wed Jan 21 03:59:57 UTC 2009

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.


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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