On 2012-07-25 10:54, Nick Schurch wrote:
Both of those produce the same error... or at least they did until we
realised that path for R was wrong. we had it installed in
/sw/bin/R2.15.0 but the Renviron file was in /sw/bin/R2.15.0/lib64/R.
Setting R_HOME to this has sorted it.
Now I have the entirely different issue of rpy2 not working with R2.15
(ignore the 2.11 typo I stuck in my original email). I get:
Error in identical(env, as.environment(i)) :
6 arguments passed to .Internal(identical) which requires 5
In addition: Warning message:
In attach(NULL, name = "Autoloads") : bytecode version mismatch; using
eval
Traceback (most recent call last):
File "./test-rpy2.py", line 5, in <module>
import rpy2.robjects as robjects
File "/sw/lib/python2.6/site-packages/rpy2/robjects/__init__.py",
line 17, in <module>
from rpy2.robjects.robject import RObjectMixin, RObject
File "/sw/lib/python2.6/site-packages/rpy2/robjects/robject.py",
line 9, in <module>
class RObjectMixin(object):
File "/sw/lib/python2.6/site-packages/rpy2/robjects/robject.py",
line 22, in RObjectMixin
__show = rpy2.rinterface.baseenv.get("show")
LookupError: 'show' not found
So it looks like it just doesn't work with the latest stable R
version, or the development R version (2.16).
I am developing / testing against the latest R. I would look to me like
there is further mix-up on your system.
A google search on "LookupError: 'show' not found" returns the following
as the first suggestion here:
https://bitbucket.org/lgautier/rpy2/issue/46/lookuperror-show-not-found
Unfortunately every time I/we come across an issue with an R package,
the standard response from the developers is usual "why aren't you
using the latest/development version of R? Try that." So having rpy2
not support these versions is a really big barrier to using it. Are
there plans to try and make rpy2 2.15/devel compatible?
May be after your sort out your local install ?
;-)
L.
Nick
On 24 July 2012 16:05, Laurent Gautier <lgaut...@gmail.com
<mailto:lgaut...@gmail.com>> wrote:
May be a mismatch between the R library rpy2 was built against. It
should not segfault thought.
Can you try:
import rpy2.rinterface
# Does this give a version number for R that you would expect ?
print(rpy2.rinterface.R_VERSION_BUILD)
# Does this complete without a crash ?
print(rpy2.rinterface.initr())
L.
On 2012-07-24 15:09, Nick Schurch wrote:
Hi,
I've installed rpy2 (2.2.4) with python 2.6.4 against R2.11 on
centos 5.6. When I import rpy2 it works fine, but when I try to
run tests or anything else : get:
>>> import rpy2
>>> rpy2.__path__
['/local/lib/python2.6/site-packages/rpy2']
>>> import rpy2.tests
cannot find system Renviron
Fatal error: unable to open the base package
Segmentation fault
Any help greatly appreciated...
--
Cheers,
Nick Schurch
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707 <tel:%2B44%201382%20388707>
Fax: +44 1382 345 893
--
Cheers,
Nick Schurch
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707
Fax: +44 1382 345 893
<tel:%2B44%201382%20345%20893>
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Cheers,
Nick Schurch
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707 <tel:%2B44%201382%20388707>
Fax: +44 1382 345 893 <tel:%2B44%201382%20345%20893>
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