You were of couse correct. stale ldconf settings were the issue. we have it
now sucessfully running on 2.15.1! Thanks.
Have you had rpy2 successfully running vs the development (2.16) version
yet?
Nick
On 26 July 2012 06:04, Laurent Gautier <lgaut...@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.schu...@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 <lgaut...@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 <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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>>>> threat landscape has changed and how IT managers can respond. Discussions
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>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>
>>>>
>>>>
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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
>
--
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
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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