On 26 July 2012 06:04, Laurent Gautier <lgautier@gmail.com> wrote:

The thread seems to be continuing on stackoverflow:

http://stackoverflow.com/questions/11658687/ld-library-path-precendence-and-trouble-with-compiling
On Jul 25, 2012 3:23 PM, "Nick Schurch" <N.Schurch@dundee.ac.uk> wrote:
Hi

I don't think rebuilding rpy2 is the problem... We compiled rpy2 against R 2.15.0 and 2.15.1 and it still gives this error both times. Attempting to build rpy2 against R 2.16 (the development version) gives build errors.

Nick
On 25 July 2012 10:07, Laurent Gautier <lgautier@gmail.com> wrote:
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 <lgautier@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
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
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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
Fax: +44 1382 345 893
The University of Dundee is a registered Scottish Charity, No: SC015096
--
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
The University of Dundee is a registered Scottish Charity, No: SC015096