[Bioc-devel] Bioc 1.8 release status: code freeze

Seth Falcon sfalcon at fhcrc.org
Tue Apr 11 05:28:21 CEST 2006

Hi all,

An update on the release process...

Code Freeze

Today is the start of the code freeze for the Bioc 1.8 release.  

* No API changes or feature additions.

* It is OK to fix bugs, improve vignettes, and add/edit documentation.

R is beta testing

If you are updating your R sources from svn, you need to switch to the
2.3 release branch.  Given a checkout of the svn trunk, you can
do the following:

   cd ~/src/R-2.3
   svn switch https://svn.r-project.org/R/branches/R-2-3-patches

NEW Deadline for passing R CMD check without errors

The check results are here:

A number of packages are failing to build or to pass check.  If you
see red for one of your packages, please take some time to try to
address the issue.

We would like to give package developers a few more days to fix up
their packages so that we can put them in the release.  The new
deadline is 17 April.  Packages with errors on the 17th
will be dropped from the release.  The 17th is still the deadline for
removing warnings.

Notes on common errors and warnings


Biobase has new validation code for exprSets that ensures that the
column names of the expression matrix align with the row names of the
phenoData data frame.  Many errors I see in the check results are
related to this.  The solution is to update your example data and make
sure it is a valid exprSet.


Most of the warnings are documentation related.  These are _easy_ to
fix, but we need your help.  Please take a few minutes to review the
warnings for your package and update the documentation.

Finally, if you have questions or need help figuring out what is
wrong, please post to bioc-devel and we will do our best to respond in
a timely fashion.

Best Wishes,

+ seth

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