[BioC] genArise

Martin Morgan mtmorgan at fhcrc.org
Tue Aug 17 04:28:31 CEST 2010

Hi Miguel --

On 08/16/2010 05:35 PM, mcarvajal at ifc.unam.mx wrote:
> Hi, i'm Miguel and i'm working in a new version of the genArise
> software. Since it was writed for R 2.3.x, a lot of thing have changed now.
> First we updated it, and now it works fine with windows vista and 7. But
> we have a great problem, it looks like all the code uses S3 classes.
> I've read that BioConductor now requires a structured code in all
> packages, and also all should use S4 classes.

We encourage new package authors to use S4 classes. But genArise is
already in the Bioconductor repository, so it is not required in this case.

> I'm not shure if all the .R files are ok, and a great problem is that
> genArise has problems using tcltk. Can anyone tell me if it's necessary
> to update genArise structure ? Or it can be submitted to bioC again
> without changes?

Because genArise is already in Bioconductor, the package maintainer can
just update the code using svn. They don't have to re-submit the
package. Some instructions are at




I don't think you're listed as the maintainer, and you may not have the
correct permissions to check in your changes. If that's the case, then
please let me know, cc'ing the original maintainer so that I know it's
ok with them that you are taking over the package. (email me off-list if
you need clarification with this).

These sorts of questions should be sent to the Bioc-devel mailing list


where we can have more technical conversations. It might also make sense
to communicate off-list if there are big changes that you'd like help with.

If you provide more information, we can try to help with tcltk.


> Thanks a lot!
> Miguel Angel Carvajal
> Mexico
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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