On Wed, Jun 5, 2013 at 2:18 PM, John Chilton <chil...@msi.umn.edu> wrote:
> Three quick comments on this thread:
>
> - A real short-coming of my colleague JJ is that he doesn't possess a
> tenth the ego that I do, so he doesn't care, but I think it is
> important he gets credit. He did 85% of the work, and the harder 85%
> at that, so they should be called the JJ changes.
>
> - It is possible to get rpy working with newer versions of R (at least
> 3.0.0) because CloudBioLinux is configured this way and it seems to
> work for me. (Not that there aren't other problems -
> https://github.com/chapmanb/cloudbiolinux/commit/302072341696390dc1cf3ae1dd88a9c1ca35a4fa).
> CloudBioLinux is configured to get its rpy packages here
> http://watson.nci.nih.gov/cran_mirror/bin/linux/ubuntu/{precise,quantal}
> which has versions compatible with R 3.0.0.
>
> - Finally, an idea - "Death to RPY - The BoF". Everyone with a stake
> in this meets with laptops at the Galaxy conference together and we
> divvy up the remaining tools to convert (hopefully one tool per
> person). Every person is also assigned two of the existing converted
> tools to retest and clean up. As they are completed they are given to
> a core Galaxy developer (Nate, Dannon, Daniel, any volunteers?) to
> collect, re-retest, and okay. The changes are then committed all
> together at the end and the next Galaxy release contains no
> dependencies on rpy.
>
> These tools are not updated frequently, so the advantage of these all
> being upgraded in one commit before being shipped off to the tool shed
> is that an institution that is really stuck on rpy1 for whatever
> reason can just undo that single commit and keep going with the old
> tools indefinitely.
>
> If anybody with commit access signs on I will be happy create a BoF
> page and attend this.
>
> Thanks,
> -John

If you all can pull that off in Oslo, great. Otherwise a piecewise
conversion seems a sensible plan B, where both rpy (v1) and rpy2
are installed and things are updated on a tool by tool basis.

The BoF group might also have some collective wisdom on how
to deal with the question of multiple versions of R/BioConductor
given this is important for reproducibility of many more complex
and rapidly developed R tools.

Peter
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