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Revision: 393 http://rpy.svn.sourceforge.net/rpy/?rev=393&view=rev Author: warnes Date: 2008-01-02 09:34:28 -0800 (Wed, 02 Jan 2008) Log Message: --- Minor code reformatting in io.c Modified Paths: -- trunk/rpy/src/io.c Modified: trunk/rpy/src/

[Rpy] SF.net SVN: rpy: [394] trunk/rpy

Revision: 394 http://rpy.svn.sourceforge.net/rpy/?rev=394&view=rev Author: warnes Date: 2008-01-02 09:57:04 -0800 (Wed, 02 Jan 2008) Log Message: --- Add code to export 'Robj' type Modified Paths: -- trunk/rpy/rpy.py trunk/rpy/src/rpymodu

[Rpy] SF.net SVN: rpy: [395] trunk/rpy/tests/test_sigint.py

Revision: 395 http://rpy.svn.sourceforge.net/rpy/?rev=395&view=rev Author: warnes Date: 2008-01-07 08:01:22 -0800 (Mon, 07 Jan 2008) Log Message: --- Add 1 second sleep to interrupt test to allow time for interrupt delivery Modified Paths: -- trunk

[Rpy] SF.net SVN: rpy: [396] trunk/rpy/src/rpymodule.c

Revision: 396 http://rpy.svn.sourceforge.net/rpy/?rev=396&view=rev Author: warnes Date: 2008-01-07 08:03:16 -0800 (Mon, 07 Jan 2008) Log Message: --- Add ability to pass command-line argumnents to init_embedded_win32 Modified Paths: -- trunk/rpy

[Rpy] SF.net SVN: rpy: [397] trunk/rpy/src/rpymodule.c

Revision: 397 http://rpy.svn.sourceforge.net/rpy/?rev=397&view=rev Author: warnes Date: 2008-01-07 09:16:11 -0800 (Mon, 07 Jan 2008) Log Message: --- Correct mismatch between declaration and definition of init_embedded_win32 Modified Paths: -- trunk

[Rpy] SF.net SVN: rpy: [401] trunk/rpy/rpy_tools.py

Revision: 401 http://rpy.svn.sourceforge.net/rpy/?rev=401&view=rev Author: warnes Date: 2008-01-25 12:14:00 -0800 (Fri, 25 Jan 2008) Log Message: --- Correct name of runtime exception Modified Paths: -- trunk/rpy/rpy_tools.py Modified: trunk

Re: [Rpy] r.predict()

The basic problem is that by default, RPy converts objects returned to python to a python object. Unfortunately, this conversion loses some information, including the type of the original R object. To avoid this conversion add two lines to your code: On Feb 22, 2008, at 12:36PM , marco hof

Re: [Rpy] package : survival

The basic problem is that "survfit" is using deparse() to try to get the name of the Surv() object so it can generate an R formula. Unfortunately, this object doesn't have a name in R's namespace, so deparse() gets the structure representation instead of the name, and then things fail.

Re: [Rpy] Rpy handling kmeans

Hello Ding, It appears that either you don't have numpy properly installed, or that your copy of rpy was compiled without numpy support. A simple workaround for this specific case would be to turn of conversion of r to python objects, so that the object 'x' remains an r matrix, rather than

Re: [Rpy] rpy crashes on graphics

This bug should be corrected in the latest version of rpy. What version are you using? -G On Feb 28, 2008, at 10:39AM , Wacek Kusnierczyk wrote: > Hi, > > Having used rpy for just a while on Fedora 7, python 2.5, I discover > that it crashes on graphics functions such as plot, hist, etc. > >

Re: [Rpy] SF.net SVN: rpy: [411]trunk/sandbox/rpy_nextgen/rinterface/rinterface.c

Wow, Laurent, you've been doing a lot of work! On Mar 2, 2008, at 2:52PM , <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> wrote: > (there is something odd going on, with variable names > at the Python level suddenly pointing to nowhere - and > this often ends in a segfault :/ ) Probably R is garbage c

Re: [Rpy] read csv in python, and pass it on to R?

You can pass the read data directly to R. Probably the best way to do this is to construct a python list containing one vector per column. Call as.data.frame() on the list, and then proceed. For example: from rpy import * set_default_mode(NO_CONVERSION) data = [ [

Re: [Rpy] Wiki for RPy Documentation?

Hi All, I think it is a good idea to use a Wiki to help develop documentation. I've enabled Wiki support over at sourceforge for rpy at http://rpy.wiki.sourceforge.net/ but I don't have time to try to pull the existing documentation in there. Of course, patches against the existin

Re: [Rpy] change RHOME

If you explicitly set the RHOME environment variable to point to the R 2.4.1 directory, rpy will use that RHOME and hence R 2.4.1. -Greg On Apr 10, 2008, at 5:53AM , Eloi Ribeiro wrote: Dear list, We are facing the fowling problem. Every thing worked fine while we had Python 2.4 + R 2.

Re: [Rpy] Error during wrapup: C stack usage is too close to thelimit

Hi All, I'm sorry to hear that the C stack limit issue has arisen again. I'll check the source code to see if the fix that we put in for RC3 has gotten removed or disabled somehow. -Greg On Apr 9, 2008, at 2:44PM , Laurent Gautier wrote: I can reproduce it with python-2.5 / R-2.6.1 as

Re: [Rpy] Error during wrapup: C stack usage is too close tothelimit

. -G On Apr 10, 2008, at 9:17AM , Gregory Warnes wrote: Hi All, I'm sorry to hear that the C stack limit issue has arisen again. I'll check the source code to see if the fix that we put in for RC3 has gotten removed or disabled somehow. -Greg On Apr 9, 2008, at 2:44PM , Laure

Re: [Rpy] installing rpy on a max running osx10.4

Hi Mark I do my rpy development on OSX 10.4, using python 2.4.2. To install rpy, just download and unpack the source .tar.gz file, then run python setup.py build sudo python setup.py install you'll probably want to ensure that Numpy is installed before you do this so you

Re: [Rpy] making a data.frame with parameters in a fixed order

Hello Andrew, The basic problem you are encountering is that python uses a dictionary to store named parameters to function calls. Python's dictionaries don't preserve order, just name-value correspondence. As a consequence calling an R function with named arguments loses the ordering.

Re: [Rpy] undefined symbol: KillAllDevices

The fix for this bug has been submitted to SVN. -G On May 12, 2008, at 2:26PM , John Reid wrote: Well I seemed to have fixed it by changing the call to KillAllDevices() in rpymodule.c to Rf_KillAllDevices() as is defined in libR.so. Perhaps there's a better way? Thanks for a great rpy pac

Re: [Rpy] Another Mac install question

The standard Mac version of R includes the necessary shared library, hence it is not necesary to do this. You should be able to simply run cd /path/to/rpy/source/code/ python setup.py build sudo python setup.py install and everything should install properly, at lea

Re: [Rpy] again installation on Mac OS X

Hi Ernesto, These warning messages are normal, albeit annoying.I've just made commited changes to the the SVN repository to avoid the ones from rpymodule.c and io.c, so this should be less of a problem in the future. -Greg On May 14, 2008, at 3:34AM , Ernesto wrote: Dear all, I'm

Re: [Rpy] Version 1.0.3 now available

Too bad. I guess I'll have to either add code to look for libRlapack.so in the appropriate directory. Know of any simple way to do this? -G On May 14, 2008, at 10:16AM , Dirk Eddelbuettel wrote: Hi Greg, On Wed, May 14, 2008 at 10:08:29AM -0400, Gregory. R. Warnes wrote: &

Re: [Rpy] Version 1.0.3 now available

I just committed a change to use R CMD config LAPACK_LIBS. Can you check if it behaves properly? -G On May 14, 2008, at 1:14PM , Dirk Eddelbuettel wrote: On Wed, May 14, 2008 at 01:06:38PM -0400, Gregory Warnes wrote: > Too bad. > > I guess I'll have to either add co

Re: [Rpy] Version 1.0.3 now available

Yea! On May 14, 2008, at 3:08PM , Dirk Eddelbuettel wrote: On Wed, May 14, 2008 at 02:36:27PM -0400, Gregory Warnes wrote: > I just committed a change to use R CMD config LAPACK_LIBS. Can you > check if it behaves properly? I get the commit emails, so I just hand-applied the changes

Re: [Rpy] Install successfully once, but fail afterward

Hmm. Does rerunning the install make a difference? -G On May 14, 2008, at 4:44PM , Manu Hack wrote: Hi, I just installed R and rpy on Opensuse 10.3. I managed to get it work once. But then all of a sudden it won't work again. Here is the info. I compiled R-2.7.0 with configure --en

Re: [Rpy] Install successfully once, but fail afterward

Is there a difference in the environment variables, particularly the value of RHOME? -G On May 14, 2008, at 5:39PM , Manu Hack wrote: On Wed, May 14, 2008 at 4:49 PM, Gregory Warnes <[EMAIL PROTECTED]> wrote: Hmm. Does rerunning the install make a difference? -G No, on

Re: [Rpy] filled.contour

Hello Lars, You will need to create an R function to accomplish the needed task. One way is to put everything into one bug R function: from rpy import r r.pdf(filename,onefile=r.TRUE, width = 7.8, height = 7,) my_contour = r(""" function(x, y, z, n=20) { Lab.palette <- colorR

Re: [Rpy] Install successfully once, but fail afterward

. -G On May 14, 2008, at 6:08PM , Manu Hack wrote: On Wed, May 14, 2008 at 5:50 PM, Gregory Warnes <[EMAIL PROTECTED]> wrote: Is there a difference in the environment variables, particularly the value of RHOME? -G No, RHOME are the same. On May 14, 2008, at 5:39PM , Manu H

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