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






On Wed, Jun 5, 2013 at 4:23 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Wed, Jun 5, 2013 at 9:42 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>> Hi Sarah
>>
>> you need to install the rpy module:
>>
>> http://rpy.sourceforge.net/rpy.html
>>
>>
>> As a warning: we have been struggling to get rpy to work with newer versions
>> of R. In or experience in only works with R version 2.9 and older. Thanks to
>> a recent effort of our sysadmin, we can now use it with 2.15 - which is
>> good, but not great, as our default version of R is now 3.0
>
> According to the rpy list, using the latest code from SVN
> you should be able to get rpy v1 to work under R 3.0.1,
> http://sourceforge.net/mailarchive/message.php?msg_id=30999482
>
>> Although we haven't started to us it, I recommend using rpy2:
>>
>> http://rpy.sourceforge.net/rpy2.html
>
> Indeed - rpy v1 is still being maintained in SVN, but
> hasn't had an official release with these fixed for
> over two years.
>
>> Most tools have been refactored by John Chilton
>>
>> see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html
>
> We're not making heavy use of rpy in Galaxy yet, but I
> hope John's good work switching to rpy2 gets integrated
> soon.
>
> Peter
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