On Wed, Jun 5, 2013 at 9:42 AM, Hans-Rudolf Hotz <hrh@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

On Wed, Jun 5, 2013 at 2:18 PM, John Chilton <chilton@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/302072341696390dc1cf3ae1dd8...). 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

Thanks a lot for these explantions, I have downloded refactored tools (rpy2 is more suited to our R version). Unfortunatly, galaxy still do not import rpy2 .. Traceback (most recent call last): File "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py", line 6, in <module> import rpy2.robjects as robjects ImportError: No module named rpy2.robjects Moreover our rpy2 module is avalaible and listed in our python. Maybe a problem with Python ? Thanks in advance, Sarah Hans-Rudolf Hotz a écrit :

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

Although we haven't started to us it, I recommend using rpy2:

http://rpy.sourceforge.net/rpy2.html

Most tools have been refactored by John Chilton

see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html

Regards, Hans-Rudolf

On 06/05/2013 10:19 AM, Sarah Maman wrote:

...

Hello,

Some Galaxy tools failed to import rpy module and displays the following message:

Traceback (most recent call last): File "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py", line 5, in <module> from rpy import * ImportError: No module named rpy

For instance, the tool "Regrouping" (tools/stats/grouping.py) have been refactored in 2011 by Kanwei Li to use numpy instead of rpy. And this tool runs on my local instance of Galaxy. But I would like to be able use rpy module instead of refactor the others tools.

Could you, please, help me to understand why the eggs ' import does not allow the use of rpy module? How to debug these tools?

Thnaks in advance, Sarah

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