[Rpy] Error loading bioconductor affy library..
Hi guys, I'm getting this error below when I try to load the bioconductor
affy library through rpy. It loads find in R though. Its a 64 bit opensuse
system. Any ideas would be greatly appreciated! Paul.
>>> from rpy import r
>>> r('library("affy")')
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)'.
Traceback (most recent call last):
File "", line 1, in
File "/usr/local/lib/python2.5/site-packages/rpy.py", line 322, in
__call__
return self.eval(self.parse(text=s))
rpy.RPy_RException: Error: package/namespace load failed for 'affy'
sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
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[Rpy] rpy syntax error...
Dear Rpythoners,
I'm having a problem using an R package called 'pvclust' from python. I have
rpy installed and things look like they are fine. The pvclust package loads
fine with r.library('pvclust'), but when I do the following command:
r.pvclust(data, method.hclust="complete", method.dist="correlation",
nboot=100)
I get the following error message:
SyntaxError: keyword can't be an expression
I had a ferret around on the web and found a similar problem to this on this
list previously, but the answer (which in this case would translate 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,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707
Fax: +44 1382 345 893
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Re: [Rpy] Error loading bioconductor affy library..
It might not be an answer to your exact problem, but it appears to work
with rpy2 (packaged for opensuse).
>>> from ryp2.robjects import r
>>> r.library("affy")
rpy2-2.1.x-dev is introducing a Python package-like approach:
>>> from rpy2.robjects.packages import importr
>>> affy = importr("affy") # import the affy package
>>> tuple(affy.bgcorrect_methods())
('mas', 'none', 'rma')
L.
Paul Geeleher wrote:
> Hi guys, I'm getting this error below when I try to load the
> bioconductor affy library through rpy. It loads find in R though. Its a
> 64 bit opensuse system. Any ideas would be greatly appreciated! Paul.
>
> >>> from rpy import r
> >>> r('library("affy")')
> 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)'.
>
> Traceback (most recent call last):
> File "", line 1, in
> File "/usr/local/lib/python2.5/site-packages/rpy.py", line 322, in
> __call__
> return self.eval(self.parse(text=s))
> rpy.RPy_RException: Error: package/namespace load failed for 'affy'
>
>
>
> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
>
>
>
>
> --
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>
>
>
>
> ___
> rpy-list mailing list
> rpy-list@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rpy-list
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Re: [Rpy] rpy syntax error...
On Fri, Sep 11, 2009 at 5:18 PM, Nick Schurch wrote:
> Dear Rpythoners,
>
> I'm having a problem using an R package called 'pvclust' from python. I have
> rpy installed and things look like they are fine. The pvclust package loads
> fine with r.library('pvclust'), but when I do the following command:
>
> r.pvclust(data, method.hclust="complete", method.dist="correlation",
> nboot=100)
Try:
r.pvclust(data, method.hclust="complete", method_dist="correlation",
nboot=100)
> I get the following error message:
>
> SyntaxError: keyword can't be an expression
>
> I had a ferret around on the web and found a similar problem to this on this
> list previously, but the answer (which in this case would translate to:
> "'hclust' is an attribute of the object 'method'") is completely greek to
> me.
In Python, the dot means access a method/property of an object.
In R, a dot is just another character in a variable or function name.
Thus rpy maps "_" to "." to allow simple access to these otherwise
invalid R names from within Python. This is in the documentation ;)
Peter
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