Dear Galaxy devs,

We are in the process of deploying Galaxy internally here at AgResearch, and I am currently installing required dependencies.  My question relates to RPy.  It seems that RPy2 is not yet supported by Galaxy, so we’re stuck with RPy 1.0.3a, and this seems to have rusted quite badly.  (I note however that the remarks previously made on the Galaxy lists about changes required to RPy appear to have been rolled into 1.0.3a.)

After installing RPy 1.0.3a, I ran the bundled test suite.  Many tests succeed, but there are several errors, in the following categories:

1.  Errors about numpy, e.g. object of type numpy.int64 has no len()  (Maybe numpy has changed since RPy 1.0.3a was written.  I am using numpy 1.4.1 on CentOS 6.)

2.  Errors due to missing files, e.g. logit.r and table.txt test data files do not appear to ship with RPy-1.0.3a (!)

3.  An error in testLapackLoad, which may be because of (2), I’m not sure yet.

4.  An R object index out of range error in testGetItemSlice, which looks quite serious.

So here’s my question.  Just how much of RPy has to work, for its use in Galaxy to be OK?

I attach my RPy test suite output in case anyone is (a) interested, (b) has any useful comments.

cheers,

Simon

Simon Guest

Senior UNIX Technical Consultant

AgResearch, NZ