[Bioc-devel] Update on upcoming BioC 1.9 release

Seth Falcon sfalcon at fhcrc.org
Sun Sep 10 00:11:59 CEST 2006

Hi all,

A few updates regarding the upcoming release:

1. R 2.4.0 alpha is now available and you should start using it to
   test your packages (see notes below).

2. The nightly builds have switched to R 2.4.0 alpha.  Results are in
   the usual location: http://www.bioconductor.org/checkResults/1.9/
   If you have questions about error or warning messages, please post
   them to this list.

3. Updated annotation data packages are available for testing.  One
   major change is that the <chip>LOCUSID env is now deprecated in favor
   of <chip>ENTREZID env.

4. The eSet superclass in Biobase has a new featureData slot as was
   requested at the developer meeting at BioC2006.  This will have an
   impact on all subclasses of eSet.  In particular, serialized
   instances will need to be updated.  The updateObject method in
   Biobase should help with this.

Notes on R 2.4.0 alpha

R 2.4.0 alpha contains many improvement to the S4 class system.
Unfortunately, the improvements require that:

1. All packages that use S4 (have a dependency on the methods
   packages) need to be reinstalled.  Building from source will be
   most reliable until the binary builds stabilize.  We have just
   begun building Windows binaries for 2.4.0 alpha, but won't have a
   clean collection of binary packages until later next week.

2. All serialized S4 instances be recreated using the new code.  The
   updateObject method in Biobase may be useful, but in the end you
   may need to address this by hand.

3. As a result of (2), we need to rebuild all experiment data
   packages.  Our plan is to update these packages on Monday along
   with as many of the packages maintained by the Biocore Team as
   possible.  This will address some of the current errors being
   reported in yesterday's build report.

+ seth

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