[Rpy] rpy2 error
Hi all, with rpy2-2.3.9 and R-3.0.2 on Windows XP sp3 I am faced with the error described in the 7zip added. Could any help / tip be given ? Best regards. Pacheco. Sreen.7z Description: Binary data -- ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
[Rpy] Rpy2 error when trying to import a library
Hi,
I am getting this weird error when I try to import the affy package from
python using Rpy2. I am using R version 2.10.1 and Rpy2 2.1.3.
The piece of code that is causing it is r.library('simpleaffy'') and the
error I am getting:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/usr/lib64/R/library/affyio/libs/affyio.so':
/usr/lib64/R/library/affyio/libs/affyio.so: undefined symbol:
R_ClassSymbol
Error: package 'affy' could not be loaded
Traceback (most recent call last):
File run.py, line 254, in module
doMicroArrayQC( Exon_FF_covdesc.txt )
File run.py, line 143, in doMicroArrayQC
r.library('simpleaffy')
File
/home/fong/lib64/python2.6/site-packages/rpy2/robjects/functions.py, line
83, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args,
**kwargs)
File
/home/fong/lib64/python2.6/site-packages/rpy2/robjects/functions.py, line
35, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error: package 'affy' could not be loaded
Any ideas on what is going on?
Fong
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Re: [Rpy] rpy2 error when loading 'oligo?
oligo is loading fine from rpy2 here.
- What OS are you using ? (from the paths in the error message that's an
UNIX-like, but more details is sometimes helpful)
- Do you have several versions of R installed on your system ? (and rpy2
somehow calling a different one from the one you get when writting R
in your shell)
L.
Peng Yu wrote:
On Sun, Sep 27, 2009 at 7:48 AM, Sean Davis seand...@gmail.com wrote:
On Sun, Sep 27, 2009 at 8:10 AM, Peng Yu pengyu...@gmail.com wrote:
Hi,
My rpy2 is of version 2.0.7.
I got the following error when I load 'oligo'. Can somebody let me
know how to fix the problem?
Regards,
Peng
from rpy2.robjects import r
r.library('oligo')
Loading required package: oligoClasses
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation(Biobase)' and for packages 'citation(pkgname)'.
Loading required package: preprocessCore
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/usr/local/lib64/R/library/affxparser/libs/affxparser.so':
/usr/local/lib64/R/library/affxparser/libs/affxparser.so: undefined
symbol: R_NilValue
Error: package/namespace load failed for 'oligo'
This looks like a problem from the R side. Can you load the oligo
package from R?
Yes. Shall reinstall R in my system?
library(oligo)
Loading required package: oligoClasses
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation(Biobase)' and for packages 'citation(pkgname)'.
Loading required package: preprocessCore
Welcome to oligo version 1.8.1
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[Rpy] rpy2 error when loading 'oligo?
Hi,
My rpy2 is of version 2.0.7.
I got the following error when I load 'oligo'. Can somebody let me
know how to fix the problem?
Regards,
Peng
from rpy2.robjects import r
r.library('oligo')
Loading required package: oligoClasses
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation(Biobase)' and for packages 'citation(pkgname)'.
Loading required package: preprocessCore
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/usr/local/lib64/R/library/affxparser/libs/affxparser.so':
/usr/local/lib64/R/library/affxparser/libs/affxparser.so: undefined
symbol: R_NilValue
Error: package/namespace load failed for 'oligo'
Traceback (most recent call last):
File stdin, line 1, in module
File
/home/pengy/utility/linux/opt/Python-2.6.2/lib/python2.6/site-packages/rpy2/robjects/__init__.py,
line 423, in __call__
res = super(RFunction, self).__call__(*new_args, **new_kwargs)
rinterface.RRuntimeError: Error: package/namespace load failed for 'oligo'
r.library('graphics')
RVector - Python:0x2fa20950 / R:0x1efdcbc0
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Re: [Rpy] rpy2 error when loading 'oligo?
On Sun, Sep 27, 2009 at 7:48 AM, Sean Davis seand...@gmail.com wrote:
On Sun, Sep 27, 2009 at 8:10 AM, Peng Yu pengyu...@gmail.com wrote:
Hi,
My rpy2 is of version 2.0.7.
I got the following error when I load 'oligo'. Can somebody let me
know how to fix the problem?
Regards,
Peng
from rpy2.robjects import r
r.library('oligo')
Loading required package: oligoClasses
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation(Biobase)' and for packages 'citation(pkgname)'.
Loading required package: preprocessCore
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/usr/local/lib64/R/library/affxparser/libs/affxparser.so':
/usr/local/lib64/R/library/affxparser/libs/affxparser.so: undefined
symbol: R_NilValue
Error: package/namespace load failed for 'oligo'
This looks like a problem from the R side. Can you load the oligo
package from R?
Yes. Shall reinstall R in my system?
library(oligo)
Loading required package: oligoClasses
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation(Biobase)' and for packages 'citation(pkgname)'.
Loading required package: preprocessCore
Welcome to oligo version 1.8.1
--
Come build with us! The BlackBerryreg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9#45;12, 2009. Register now#33;
http://p.sf.net/sfu/devconf
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