Re: [Rpy] Fwd: problems with rpy2...

on stackoverflow: > > > http://stackoverflow.com/questions/11658687/ld-library-path-precendence-and-trouble-with-compiling > On Jul 25, 2012 3:23 PM, "Nick Schurch" wrote: > >> Hi >> >> I don't think rebuilding rpy2 is the problem... We compiled rpy2 aga

Re: [Rpy] Fwd: problems with rpy2...

12-07-25 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. >

Re: [Rpy] Fwd: problems with rpy2...

t 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. > > &g

[Rpy] Fwd: problems with rpy2...

ort 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

Re: [Rpy] Problems with DESeq library in rpy

ject has no attribute 'estimateVarianceFunction' >>> I'm not sure why its doing this, but I don't thing importr('DESeq') is loading everything it needs. Under rpy v1 I was using >>> r.library("DESeq") Loading required package: locfit Loadin

Re: [Rpy] Problems with DESeq library in rpy

14:37, Laurent Gautier wrote: > ** > Did you terminate your session and restarted ? > If not, it won't work until you clear "estimateVarianceFunction" from the > current R GlobalEnv. > > > L. > > > > > On 2011-10-07 15:33, Nick Schurch wrote: >

[Rpy] Problems with DESeq library in rpy

, using exactly the same version of R (2.13.1) and exactly the same version of the DESeq library (1.4.1) on the same machine. Any help would be gratefully appreciated -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dunde

Re: [Rpy] More rpy2 install woes...

> The one failed tests is a forced failure, and a visual inspection is > hopefully informative enough. > > self.assertTrue(False) # arrays of unicode characters causing segfault > > self.assertTrue(False): "assert that False is True"; this is the signature > of forced failed test. This is followed

[Rpy] More rpy2 install woes...

call last): File "rpy2/robjects/tests/testNumpyConversions.py", line 53, in testVectorUnicodeCharacter self.assertTrue(False) # arrays of unicode characters causing segfault AssertionError ------ Ran 107 tests in 0.732s FAILED (failures=1) Anyone have any ideas, before I ditch rpy2 and re

[Rpy] rpy2 2.10 install...

g/rpy2/rinterface/__init__.py", line 75, in File "build/bdist.linux-i686/egg/rpy2/rinterface/rinterface.py", line 7, in File "build/bdist.linux-i686/egg/rpy2/rinterface/rinterface.py", line 3, in __bootstrap__ ImportError: No module named pkg_resources am I missing

[Rpy] Stopping rpy remembering functions...

ustomers whose forename is Blogs. The user defined R-function defined from the first run is not overwritten by the second run. Is there any way to clear an R-function from rpys R instance? -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life

Re: [Rpy] accessing data within a dataframe

rt it back into an R object to feed into pvpick, but when I try this somthing isn't right about the conversion back and it falls over. There must be a way to edit the robj without requiring a conversion... This really should be simple - I'm amazed that it isn't; or am I missing someth

[Rpy] snow from within rpy

data=data, method_hclust="complete", method_dist="euclidean", nboot=100) Anyone have any idea how (or whether its even possible) to get this working? -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5E

[Rpy] accessing data within a dataframe

ly want to convert the robj to a python object - I just want to know how I can reference the data within the dataframe. Any help would be greatly appreciated. -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Scien

Re: [Rpy] rpy syntax error...

o predefine result as an rpy object or something? -- 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

[Rpy] rpy syntax error...

nslate to: "'hclust' is an attribute of the object 'method'") is completely greek to me. Thanks in advance for your help! -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, D