[Bioc-devel] exprSet and friends

Hi,

what about creating a package 'BioCDeprecated' and move those classes
and function there?  Packages making use of deprecated
classes/functions can then depend on that package.  This will make it
clear for everyone that there are deprecated things being used.  It
would also clean out the code and the documentation of a few BioC
packages.  BioCDeprecated can be used for other purposes in future
release cycles as well.

A safe step towards the above is to extract the above package and make
Biobase dependent on it.  That should be totally transparent for all
packages as is today.  When that is working (by looking at the nightly
builds), one could scan packages for 'exprSet' and add BioCDeprecated
to Depends: in DESCRIPTION.  As a final step one removes the
dependency Biobase -> BioCDeprecated and then nightly builds would
tell us what remaining packages has to have their DESCRIPTION updated.

Cheers

Henrik

Hi,
   I would like to get some comments on whether we can safely make all
exprSet methods defunct, or of folks think we want yet one more cycle?
I have found a few more lurking around recently, and I think it would
help us to get them all expunged, sooner rather than later.

   thanks
    Robert

--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org

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