New local Galaxy Install: Problem with grouping -- rpy issue
Hello All, When running a grouping on a data set via the Join, Subtract, Grouping menu, I receive this error. An error occurred running this job: *Traceback (most recent call last): File "/opt/Bio/galaxy_dist/tools/stats/grouping.py", line 7, in ? from rpy import * ImportError: No module named rpy *I'm having the hardest time figuring out which R version with what version of Rpy to use. So far I've tried rpy-1.0.3, rpy2-2.0.6, with Rpackages 2.7.2 and 2.9.1. I've gotten both rpackages to compiled with the --enable-R-shlib option and I have put it in my $PATH. However, when trying to install either of they rpy packages, they complain about missing header file RGraphics.h, Rdevices.h, and more. Does anyone have a known good configuration to get this module working with galaxy? Which R package with which rpy version should I be using? Thanks, Hans Vasquez-Gross
Hans Vasquez-Gross wrote:
/I'm having the hardest time figuring out which R version with what version of Rpy to use. So far I've tried rpy-1.0.3, rpy2-2.0.6, with Rpackages 2.7.2 and 2.9.1. I've gotten both rpackages to compiled with the --enable-R-shlib option and I have put it in my $PATH. However, when trying to install either of they rpy packages, they complain about missing header file RGraphics.h, Rdevices.h, and more. Does anyone have a known good configuration to get this module working with galaxy? Which R package with which rpy version should I be using?
Hi Hans, You'll need to use RPy 1.0.3, but it hasn't been updated to make use of newer versions of R. The solution to the header problems is simply to remove the includes to those headers. In the newer versions of R, those headers have been consolidated into headers which are already included by RPy. --nate
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Hans Vasquez-Gross -
Nate Coraor