Yes this is a bizarre error that I had been getting. It was difficult
to track down
exactly where the bug came from, but it was somehow related to the C
stack limit size,
which was evidently too small and causing the R process to crash ...
only when used in
conjunction with RPy and Django (bi
rs
D[k]=[x.encode("UTF-8") for x in v]
return D
Quoting Toby HOCKING :
> Hi fellow RPy-ers, long time no chat, hope everything is going well
> for you all,
>
> Maybe you guys remember me --- I emailed the list a year or so ago and
> I had a problem with un
Hi fellow RPy-ers, long time no chat, hope everything is going well
for you all,
Maybe you guys remember me --- I emailed the list a year or so ago and
I had a problem with unicode string conversion from Python to R using
RPy1. Here is a webpage I just found with the relevant email
http://a
One more thing: in R it seems accent strings have the encoding "UTF-8"
whereas python strings come into R always with an unknown encoding.
Maybe this has something to do with it?
thock...@stagiaire-desktop:~/rpy$ R
> Encoding("c")
[1] "unknown"
> Encoding("ç")
[1] "UTF-8"
thock...@stagiaire-d
c. The oldest version that worked without messing
with stack usage limits in the shell was R-2.2.1.
-Original Message-
From: Laurent Gautier [mailto:[EMAIL PROTECTED]
Sent: Monday, July 14, 2008 8:40 AM
To: Toby Hocking
Cc: RPy help, support and design discussion list
Subject: Re: [Rpy] r
-2.7 with rpy and
Apache2/mod_python/Django.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Toby Hocking
Sent: Wednesday, June 25, 2008 9:29 AM
To: RPy help, support and design discussion list
Subject: Re: [Rpy] rpy and mod_python problem
I'm inclin
Gautier
Sent: Wednesday, June 25, 2008 11:45 AM
To: RPy help, support and design discussion list
Subject: Re: [Rpy] rpy and mod_python problem
2008/6/25 Toby Hocking <[EMAIL PROTECTED]>:
> I'm inclined to think that it is NOT an inherent incompatibility problem with
> mod_python and R
I'm inclined to think that it is NOT an inherent incompatibility problem with
mod_python and RPy since I have a working Rpy/apache/mod_python system on top
of Django. Relevant package versions for the working system are:
Django-rev7716
Apache-2.0.55-4ubuntu2.3
mod_python-3.1.4-0ubuntu1.1
R-2.2.1
Hi Christof, did you ever resolve this problem? I am experiencing it now, and I
was wondering what you did for a solution/workaround. Thanks.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Christof
Winter
Sent: Wednesday, June 11, 2008 12:58 PM
To: rpy-list
You also may want to try to use the PDF graphics device in R (function pdf) and
then use convert (http://imagemagick.org) to make a PNG for viewing on the web.
This is the method I have used with great success in my Django-dataplot package
(http://django-dataplot.sf.net), which is a RPy plotting
These new slice changes are breaking my rpy compilation:
gcc -pthread -fno-strict-aliasing -g -Wall -fPIC -DWITH_NUMERIC=1
-DRPY_SHNAME=_rpy2021 -DINIT_RPY=init_rpy2021 -UPRE_2_2 -I/usr/lib/R/include
-Isrc -I/usr/share/R/include -I/usr/include/python2.4 -c src/rpymodule2021.c -o
build/temp.linu
m a purist, but this juste looks like hacking... isn't it a more
straight forward way to do it ?
Thank you again, your solution definetly solve my issue!!
-Etienne
Toby Hocking a écrit :
> Why don't you put your R code in file.R:
>
> library('stats')
> my.summary
Why don't you put your R code in file.R:
library('stats')
my.summary = function(Res) {
av <- aov( score~factor+Error(id_subject/factor), data=Res)
summary(av)
}
then from python:
r.source("file.R")
r.my_summary(Res)
???
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PRO
Your problem is that R can't find your LAPACK library.
Could it be that your use of forward slashes instead of backslashes here is
confusing windows?? Try to use backslashes instead and see what happens.
'C:\Program Files\R\R-2.6.1/modules//lapack.dll':
-Original Message-
From: [EMA
That worked, thanks! I was missing the python2.4-dev libraries (duh!)
Toby
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Dirk
Eddelbuettel
Sent: Monday, November 05, 2007 8:14 PM
To: RPy help, support and design discussion list
Subject: Re: [Rpy] RPy won't
Thanks for the response, Gregory. But I need a bit more help.
So far I am using the test python code
from rpy import r
r.print_(u'')
r.print_(u' ')
By inserting print statements into the RPy C code (rpymodule.c), I have
determined that every time RPy accesses an R object, it goes through the C
Hey Erez,
I don't know any reason why you are getting that error, but maybe this will
help. You may want to check out the Biopython (biopython.org) interface to
Clustalw. I'm using rpy together with the Clustalw biopython package, and
everything seems to work fine. My package versions are:
htt
the easiest solution in my opinion is to use environment variables to tell rpy
where R is -- this also tells rpy which version of R it is using. Set the
R_HOME environment variable before starting python, i.e.
set R_HOME=S:\users-science\thocking\selex\R-2.2.1
Good luck...
-Original Message
Hi there Christian,
I find it's easiest to use rpy if you minimize the number of data conversion
steps you need. That is, write most of your code in R, wrap it in my.function,
then call it from python via
r.source("my.source.file.R")
r.my_function(args)
Rather than constructing a data frame in
search your sys.path and see if the rpy package is on it.
>>> import sys
>>> print sys.path
if not, add the path where you have rpy installed.
TDH
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Jonathan E.
Magen
Sent: Tuesday, October 31, 2006 3:44 PM
To:
Not sure about this one but it seems like you have isolated the problem to
the rpy library itself --- perhaps there is some problem with DLLs since
this is an external package?
-Original Message-
From: xianfeng song [mailto:[EMAIL PROTECTED]
Sent: Monday, September 25, 2006 9:39 AM
To: rpy
I've been experimenting with rpy for a few weeks now and it definitely seems
that you are encountering a problem that can be fixed by putting the full
path to your R executables in your PATH. Also another fix may be setting the
R_HOME environment variable to the full path to the R-2.x.y directory.
> Hi all,
>
> Just wondering if anybody can help me with the following problem.
>
> I'm running R 2.3.1 and Python 2.4, and I've got rpy to work on windows,
> but with one little glitch:
>
> Whenever I call a plotting function, the graphics window comes up and does
> the plot, but then the windo
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