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).
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?
Nick
On 24 July 2012 16:05, Laurent Gautier <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
> 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
>
> <%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
Fax: +44 1382 345 893
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
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