[with patch, positive review] set correct RHOME for rpy

[fbissey]

A problem was reported to me a month or two ago and I was hit by it when I built sage-3.0.2 from scratch (rather than by sage -upgrade). rpy didn't build because RHOME was not defined. This may be required because I have not only sage version of R but also a system provided version. After adding a line in rpy spkg-install pointing RHOME to SAGE_LOCAL/lib/R it did build without problem. However a test failed: sage -t devel/sage/sage/stats/test.py File "/home/francois/Work/SAGE/tmp/test.py", line 5:

sage: import rpy

Exception raised:

Traceback (most recent call last):

File "/home/francois/Work/SAGE/local/lib/python2.5/doctest.py", line 1228, in run

compileflags, 1) in test.globs

File "<doctest main.example_0[1]>", line 1, in <module>

import rpy###line 5:

sage: import rpy

File "/home/francois/Work/SAGE/local/lib/python2.5/site-packages/rpy.py", line 58, in <module>

RVERSION = rpy_tools.get_R_VERSION(RHOME)

File "/home/francois/Work/SAGE/local/lib/python2.5/site-packages/rpy_tools.py", line 99, in get_R_VERSION

" `%s'.\n" % rexec )

RuntimeError?: Couldn't execute the R interpreter `/usr/lib/R/bin/R'.

================ As one can see sage's rpy was trying to use the system provided R rather than sage's own. An extra line in sage-env took care of that. 2 small patch attached to cover this corner case. Note that the patches won't make any difference to people not affected by this issue.

[mabshoff]

Hi Francois,

thanks for the patches, we already had a ticket for this issue at #3011, so I am closing that as a duplicate. Please make sure in the future that you add "[with patch, needs review]" line to the Summary field and also assign a default milestone so your patch isn't slipping through the cracks. I will review this patch shortly, but it looks good as is :)

Cheers,

Michaek

[mabshoff]

Ok, both patches look good. A couple remarks:

• please post proper mercurial patches. I committed the patches in your name, but it would make applying future patches easier
• be precise, i.e. spkg-install is for the rpy.spkg - it tool me some time to figure that out.

An updated r.spkg containing all your fixes [and some more things by me like updated SPKG.txt] is available at

 http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0.3/alpha1/r-2.6.1.p17.spkg

Cheers,

Michael

[mabshoff]

Merged in Sage 3.0.3.alpha1