[Bioc-devel] exprSet and friends

Henrik Bengtsson hb at stat.berkeley.edu
Mon Sep 17 23:53:26 CEST 2007


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.



On 9/13/07, Robert Gentleman <rgentlem at fhcrc.org> wrote:
> 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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