It is possible if rpy is detecting and using a different R binary...
-Greg
> -Original Message-
> From: Luca Beltrame [mailto:luca.beltr...@marionegri.it]
> Sent: Wednesday, May 25, 2011 10:16 AM
> To: rpy-list@lists.sourceforge.net
> Subject: [Rpy] Strangeness with R.home
>
> Hello,
>
The issue is probably that your surv_time variable is being translated
'back' into a python object.
Try changing the conversion mode to NO_CONVERSION and explicitly
requesting conversion when you need to access the results in python.
I.E.
import rpy
rpy.set
Revision: 776
http://rpy.svn.sourceforge.net/rpy/?rev=776&view=rev
Author: warnes
Date: 2010-02-11 20:53:49 + (Thu, 11 Feb 2010)
Log Message:
---
Modify version regexp to allow multi-digit numbers in any section.
Modified Paths:
--
trunk
1")
in which case
r.dollar
would return the R vector containing 1, and
stackloss.r.dollar("Air.Flow")
would still work, too.
-Greg
> -Original Message-
> From: n...@vorpus.org [mailto:n...@vorpus.org] On Behalf Of Nathaniel
> Smith
> Se
Hi All,
These are the longstanding rpy rules (where 'x' represents any sequence
of valid name character in *python*, including A-Z, a-Z anywhere and 0-9
anywhere except in the first position):
python R Example
x_x x.x print_default(m) --> print.default(m)
x_
The problem is that the R object returned from
"rpy.r.matrix(range(6),nr=2)" is being automatically converted to a
python object before being passed to the transpose function.
The easiest solution is to turn off automatic conversion, and then
manually ask for conversion when you want it:
>>> impo
R is complaining because you handed the 'oneway' function a single
string parameter.
Instead of
oneway = robjects.r['oneway.test']
test = oneway("values ~ ind, data=d, var.equal=TRUE")
try this:
test = robjects.r['oneway.test(values ~ ind, data=d, var.equal=TRUE)']
or
oneway = robjects.r[
Hi Everyone,
(Yes, I'm finally coming out of hibernation...)
Another approach to the problem, and one I adopted for RSOAP, involved
pre-starting a single process which initialized R. Then anytime a
request came in, the process forked, resulting in an immediate
'ready-to-go' process to do the wor
/R version is the most needed?
Laurent
2008/12/1 Warnes, Gregory R. <[EMAIL PROTECTED]>:
> RPy 1.0 will continue to exist, and bug fixes will be made, but
feature
> enhancements will occur in RPy2, which is being so capably handled by
> Laurent. I'll try to create a Windows
Yes, we do accept Windows binary submissions.
-greg
-Original Message-
From: Peter [mailto:[EMAIL PROTECTED]
Sent: Monday, December 01, 2008 5:30 AM
To: RPy help,support and design discussion list
Subject: Re: [Rpy] future of rpy 1.0
On Mon, Dec 1, 2008 at 2:42 AM, Mario Beauchamp <[E
RPy 1.0 will continue to exist, and bug fixes will be made, but feature
enhancements will occur in RPy2, which is being so capably handled by
Laurent. I'll try to create a Windows installer for 2.8.0 later this
week.
-Greg
-Original Message-
From: Laurent Gautier [mailto:[EMAIL PROTECTED]
Use
fun = r(" function(x) { x+1 }")
-G
- Original Message -
From: Antonio Garcia-Martinez <[EMAIL PROTECTED]>
To: rpy-list@lists.sourceforge.net
Sent: Thu Nov 20 23:35:25 2008
Subject: [Rpy] uniroot, and r.function()
I'm trying to use R's uniroot function from within python. The first
[Forwarded for David Carr]
From: Carr, David [mailto:[EMAIL PROTECTED]
Sent: Tuesday, November 11, 2008 1:28 PM
Hello all,
I am preparing a lecture for next week... was going to introduce rpy2 to
the class.
But using the latest rc1 binary on Windows and I get the following
errors.
Please
Revision: 666
http://rpy.svn.sourceforge.net/rpy/?rev=666&view=rev
Author: warnes
Date: 2008-10-28 19:28:14 + (Tue, 28 Oct 2008)
Log Message:
---
Add Larent's change to the html page template (annoucing RPy2 2.0.0-a3)
Modified Paths:
--
tru
Revision: 665
http://rpy.svn.sourceforge.net/rpy/?rev=665&view=rev
Author: warnes
Date: 2008-10-28 19:16:27 + (Tue, 28 Oct 2008)
Log Message:
---
Correct link to SVN viewer
Modified Paths:
--
trunk/htdocs/svn.data
Modified: trunk/htdocs/svn.
I will try to update rpy to work with R 2.8 later this week. Feel free
to remind me if you don't see anything by Thursday evening.
-Greg
-Original Message-
From: laurent oget [mailto:[EMAIL PROTECTED]
Sent: Monday, October 20, 2008 11:43 AM
To: RPy help,support and design discussion lis
Works fine for me after removing the old fink python 2.4 so that I'm
using 2.5.1
-G
-Original Message-
From: Laurent Gautier [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 07, 2008 1:06 PM
To: Warnes, Gregory R.
Cc: rpy-list@lists.sourceforge.net
Subject: Re: [Rpy] rpy2: a
I get a similar error on my Mac Leopard system:
[Crooked-2:~/src/rpy_nextgen] warnes% python setup.py build
running build
running build_py
creating build
creating build/lib.darwin-9.4.0-i386-2.4
creating build/lib.darwin-9.4.0-i386-2.4/rpy2
copying rpy/__init__.py -> build/lib.darwin-9.4.0-i
of rpy
> (may be a class extending Python's "threading.Thread" ?)
>
This makes good sense.
-G
>
> L.
>
>
>
>
> 2008/6/26 Gregory Warnes <[EMAIL PROTECTED]>:
>> > Hi Laurent,
>> >
>> > It does seem desirable to inc
uments)
> complicated (if possible).
>
> Ideas, or help, on the matter are welcome.
>
>
> L.
>
>
>
>
> 2008/6/26 Gregory Warnes <[EMAIL PROTECTED]>:
>> >
>> > Hello Laurent,
>> >
>> > The R system itself is not thr
gt; >> 2008/6/26 laurent oget <[EMAIL PROTECTED]>:
>>>> >>> So if I want to take advantage of my two cores, i need two processes,
>>>> right?
>>>> >>>
>>>> >>> 2008/6/26 Gregory Warnes <[EMAIL PROTECTED]>:
&
ervices for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
--
Gregory R. Warnes, Ph.D
Program Director
Center for Computational Arts, Sciences, and Engineering
University of Rochester
Tel: 585
best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
--
Gregory R. Warnes, Ph.D
Program Director
Center for Computational Arts, Sciences, and Engineering
University of Rochester
Tel: 585
gt; libreadline.5.2.dylib*
> libreadline.dylib@
> ppc/
-Greg
--
Gregory R. Warnes, Ph.D
Program Director
Center for Computational Arts, Sciences, and Engineering
University of Rochester
Tel: 585-273-2794
Fax: 585-276-2097
Email: [EMAIL PROTECTED]
---
> What am I doing wrong here ?
>
> Any help is greatly appreciated.
>
> Thanks,
> Nishant
>
> -----
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services fo
tended as or should
> be construed as an offer, solicitation or recommendation to buy or sell any
> security or other financial instrument. Neither the sender, his or her
> employer nor any of their respective affiliates makes any warranties as to the
> completeness or accuracy of any of the information contained her
rpy-list@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/rpy-list
>> >
>
> -
> Check out the new SourceForge.net Ma
> Still can't get it to work... Am I missing something?
>
> b <- r("'rownames<-'")(b, a)
> TypeError: 'str' object is not callable
>
> I'm with RPy version 1.0.3 [R version 2.7.0 (2008-04-22)]
>
> Quoting Warnes, Gregory on 06/1
on... without much success.
>
> I haven't been able to use your suggestion. I always get the error:
> unexpected '[' in "["
>
> Apart from this, is <- valid python syntax? Or did you meant to say = ?
>
> An example like this in the documentation
On Jun 10, 2008, at 9:20AM , Chris Arthur wrote:
Thanks Gregory, that "y ~ ." syntax solves my problems. and allows
my to
pull out the PLSR data I wanted, but leads me to my next problem.
Glad to help.
I then try to use my model to predict the value of the matrix accFAS
predicted=r.pr
versions.
-G
On Jun 9, 2008, at 1:12PM , Dirk Eddelbuettel wrote:
On Mon, Jun 09, 2008 at 12:36:19PM -0400, Gregory Warnes wrote:
> Aside, since rpy _does_ check for specific R versions, would it
not be
> advisable for the .deb dependencies to reflect this appropriately?
I tried that
Thanks Peter, the sf.net news page has been disabled.
On Jun 9, 2008, at 10:05AM , Peter wrote:
I'm confused about why there are two different news pages:
http://rpy.sourceforge.net/news.html
This includes the new wiki announcement and the 1.0.2 release and a
lot of historical entries. Thi
You may find the forumula syntax
y ~ .
helpful. If data= is supplied to the modeling command, the single
period means 'all variables in the data frame that are not
otherwised mentioned.
As for changing he names on an existing object, you can't use the
rownames(x) <- foo syntax
Aside, since rpy _does_ check for specific R versions, would it not
be advisable for the .deb dependencies to reflect this appropriately?
-G
On Jun 8, 2008, at 1:13PM , Dirk Eddelbuettel wrote:
On 8 June 2008 at 11:15, Lars Tangvald wrote:
| Laurent Gautier skrev:
| > 2008/6/7 Dirk Edde
Makes good sense.
-G
On Jun 1, 2008, at 7:40AM , <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> wrote:
Revision: 541
http://rpy.svn.sourceforge.net/rpy/?rev=541&view=rev
Author: lgautier
Date: 2008-06-01 04:40:33 -0700 (Sun, 01 Jun 2008)
Log Message:
---
- only keep suppo
Hi Laurent,
Why not use the get_R_HOME() function in rpy_tools.py, which already
handles this for Unix and Win32. (On Win32 it checks for the proper
R registry entry for this information, then falls back to other
methods if this is not available.)
-G
On Jun 1, 2008, at 6:54AM , <[EMAI
OK, this is quite odd. Two more things to try. First, try adding
the directory containing multiarray.DLL to the PATH before running
python. Second, if this doesn't work, try running python with the -v
option and redirecting the output to a file..
-G
On May 22, 2008, at 4:21PM , James
Hmm. How about the more adventuresome
import numpy.core.multiarray
?
-Greg
On May 22, 2008, at 3:59PM , James D Dickinson wrote:
>>> import numpy
works just fine no messages or errors -
trying to import rpy results in same messages below
-James
>I think this is prob
I think this is probably a Numpy installation issue. What happens if
you issue the command
import numpy
??
-Greg
On May 22, 2008, at 1:40PM , James D Dickinson wrote:
Hi - I'm fairly new to Python and I'm having a heck of a a getting the
install of 'rPy' to go.
I downloaded th
The best way to store R objects is to use R's own 'save()' and 'load
()' functions. In order to use these, it is necessary for the
objects to be assigned to R names, so you would have something like...
from rpy import r
# code here to create objects 'a' and 'b'
r.as
.
-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
error:
rpy.py:1: RuntimeWarning: Python C API version mismatch for module
_rpy2070: This Python has API version 1013, module _rpy2070 has
version 1012.
#
Mirco
On May 18, 2008, at 10:16 PM, Warnes, Gregory R wrote:
> I've uploaded a new mac binary for 1.3.0 that supports 2.6.2 and
I've uploaded a new mac binary for 1.3.0 that supports 2.6.2 and 2.7.0.
-G
--Original Message--
From: Mirco Musolesi
To: rpy-list@lists.sourceforge.net
ReplyTo: RPy help, support and design discussion list
Sent: May 18, 2008 7:06 PM
Subject: [Rpy] Problem with the installation of rpy on M
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
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
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
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
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
Revision: 524
http://rpy.svn.sourceforge.net/rpy/?rev=524&view=rev
Author: warnes
Date: 2008-05-14 11:33:26 -0700 (Wed, 14 May 2008)
Log Message:
---
remove completed TODO entry
Modified Paths:
--
trunk/rpy/TODO
Modified: trunk/rpy/
Revision: 523
http://rpy.svn.sourceforge.net/rpy/?rev=523&view=rev
Author: warnes
Date: 2008-05-14 11:31:21 -0700 (Wed, 14 May 2008)
Log Message:
---
Use the 'R CMD config LAPACK_LIBS' command to determin the appropriate link
flags for lapack, instead of bl
Revision: 517
http://rpy.svn.sourceforge.net/rpy/?rev=517&view=rev
Author: warnes
Date: 2008-05-14 10:10:57 -0700 (Wed, 14 May 2008)
Log Message:
---
Turn off debug build flag for default installs, add todo about Rlapack/lapack
Modified Paths:
--
trunk
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:
&
Revision: 516
http://rpy.svn.sourceforge.net/rpy/?rev=516&view=rev
Author: warnes
Date: 2008-05-14 10:05:47 -0700 (Wed, 14 May 2008)
Log Message:
---
Add note about checking for Rlapack
Modified Paths:
--
trunk/rpy/TODO
Modified: trunk/rpy/
Hi Dirk,
Is it sufficient to simply add lapack to the list of libraries?
libraries=['R','Rlapack','lapack']
-Greg
On May 13, 2008, at 9:38AM , Dirk Eddelbuettel wrote:
Hi Greg,
On 12 May 2008 at 23:54, Gregory. R. Warnes wrote:
| Hi All,
|
|
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
Revision: 515
http://rpy.svn.sourceforge.net/rpy/?rev=515&view=rev
Author: warnes
Date: 2008-05-14 06:53:05 -0700 (Wed, 14 May 2008)
Log Message:
---
Minor changes to remove compilation warnings
Modified Paths:
--
trunk/rpy/src/RPy.h
trunk/rpy/src/
build this for our Windows users?
Thanks
-Greg
Gregory R. Warnes, Ph.D.
Associate Professor
Center for Biodefence Immune Modeling
and
Department of Biostatistics and Computational Biology
University of Rochester
-
Revision: 514
http://rpy.svn.sourceforge.net/rpy/?rev=514&view=rev
Author: warnes
Date: 2008-05-12 20:47:51 -0700 (Mon, 12 May 2008)
Log Message:
---
Updated for 1.0.3
Modified Paths:
--
trunk/rpy/NEWS
trunk/rpy/rpy_version.py
Modified: trunk/rpy/
Revision: 513
http://rpy.svn.sourceforge.net/rpy/?rev=513&view=rev
Author: warnes
Date: 2008-05-12 20:32:37 -0700 (Mon, 12 May 2008)
Log Message:
---
Add notes on what is necessary to build against multiple versions of R on OSX
Modified Paths:
--
trunk
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
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
Revision: 511
http://rpy.svn.sourceforge.net/rpy/?rev=511&view=rev
Author: warnes
Date: 2008-05-09 14:17:54 -0700 (Fri, 09 May 2008)
Log Message:
---
Add to TODO.
Modified Paths:
--
trunk/rpy/TODO
Modified: trunk/rpy/
Revision: 510
http://rpy.svn.sourceforge.net/rpy/?rev=510&view=rev
Author: warnes
Date: 2008-05-09 14:16:59 -0700 (Fri, 09 May 2008)
Log Message:
---
Patch to correct link problem with R-2.7.0
Modified Paths:
--
trunk/rpy/src/rpymodule.c
Modified: t
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.
Revision: 507
http://rpy.svn.sourceforge.net/rpy/?rev=507&view=rev
Author: warnes
Date: 2008-04-28 12:58:14 -0700 (Mon, 28 Apr 2008)
Log Message:
---
Fix Wiki url on news page
Modified Paths:
--
trunk/htdocs/news.data
Modified: trunk/htdocs/news.
Revision: 506
http://rpy.svn.sourceforge.net/rpy/?rev=506&view=rev
Author: warnes
Date: 2008-04-28 12:53:52 -0700 (Mon, 28 Apr 2008)
Log Message:
---
Update news items from late 2007 to present
Modified Paths:
--
trunk/htdocs/news.data
trunk/ht
Revision: 503
http://rpy.svn.sourceforge.net/rpy/?rev=503&view=rev
Author: warnes
Date: 2008-04-24 07:07:58 -0700 (Thu, 24 Apr 2008)
Log Message:
---
Remove auto-generated html file from SVN repository
Removed Paths:
-
trunk/htdocs/plotting-with-RPy.
Revision: 502
http://rpy.svn.sourceforge.net/rpy/?rev=502&view=rev
Author: warnes
Date: 2008-04-24 06:59:59 -0700 (Thu, 24 Apr 2008)
Log Message:
---
Update Windows download/install instructions to recommend NumPy rather than
Numeric
Modified P
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
Revision: 489
http://rpy.svn.sourceforge.net/rpy/?rev=489&view=rev
Author: warnes
Date: 2008-04-16 07:19:47 -0700 (Wed, 16 Apr 2008)
Log Message:
---
Fix R.__repr__() bug.
Modified Paths:
--
trunk/rpy/rpy.py
Modified: trunk/rpy/rp
Hi All,
I've uploaded RPy 1.0.2 to sourceforge. The NEWS entry for this
version is below. Importantly, this should version should (re-)
correct crashes due to issues with R's C stack checking code.
-Greg
CHANGES IN RPY 1.0.2 - 2008-04-10
-
New features:
Revision: 487
http://rpy.svn.sourceforge.net/rpy/?rev=487&view=rev
Author: warnes
Date: 2008-04-10 09:51:42 -0700 (Thu, 10 Apr 2008)
Log Message:
---
Update for RPy release 1.0.2
Modified Paths:
--
trunk/rpy/NEWS
trunk/rpy/rpy_version.py
Modi
Revision: 486
http://rpy.svn.sourceforge.net/rpy/?rev=486&view=rev
Author: warnes
Date: 2008-04-10 09:50:51 -0700 (Thu, 10 Apr 2008)
Log Message:
---
Add simple neural net example
Added Paths:
---
trunk/rpy/examples/nnet.py
Added: trunk/rpy/examples/nne
Revision: 485
http://rpy.svn.sourceforge.net/rpy/?rev=485&view=rev
Author: warnes
Date: 2008-04-10 09:49:07 -0700 (Thu, 10 Apr 2008)
Log Message:
---
Use R's internal function to clean up R temporary directory for R 2.4.0 and
later
Modif
.
-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
Revision: 484
http://rpy.svn.sourceforge.net/rpy/?rev=484&view=rev
Author: warnes
Date: 2008-04-10 06:45:34 -0700 (Thu, 10 Apr 2008)
Log Message:
---
Correct the handling of CStackLimit code.
Modified Paths:
--
trunk/rpy/src/rpymodule.c
Modified: t
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
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.
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
Revision: 475
http://rpy.svn.sourceforge.net/rpy/?rev=475&view=rev
Author: warnes
Date: 2008-04-03 16:26:50 -0700 (Thu, 03 Apr 2008)
Log Message:
---
Use failUnless / failUnlessRaises instead of assertTrue / assertRaises in
test_robj.py for compatibility with python
I've just built a version with support for 2.6.2. Look for it tomorrow.
-G
--Original Message--
From: Mark Janikas
To: rpy-list@lists.sourceforge.net
ReplyTo: RPy help, support and design discussion list
Sent: Apr 2, 2008 5:58 PM
Subject: [Rpy] rpy and R 2.6.2
Hello all,
I am new
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 = [ [
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
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.
>
>
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
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.
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
Btw, I've committed a fix to SVN for the bug that resulted in this
error message:
NameError: global name 'RuntimeExecError' is not
defined
rather than the more appropriate
RuntimeError: "Couldn't execute the R interpreter."
-Greg
---
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
During the installation of R, there is an option (on by default) to
set the R registry entries. If, for some reason, this gets
unchecked, it doesn't happen.
In any case, the problem can be solved by properly setting the RHOME
environment variable. The RHOME environment variable should poin
R itself is neither multithreaded, nor thread safe. If you want to
interact with more than one R session, you'll have to have a separate
process for each R session. I built the RSOAP tool, which includes
wrapper (called something like) LocalRSOAPConnection that wraps the
separate session
Thats odd. If you've got the setup to compile RPy, you might try
adding an explicit "--no-Rconsole" argument to the variable
"defaultargv" at the top of src/rpymodule.c and see if that makes a
difference for the 'out of the box' R.
-G
On Jan 8, 2008, at 12:11PM , Barry Rowlingson wrote:
There was also a bug in RPy's handling of unicode strings until 1.0,
so make sure you have a recent version of RPy as well.
-G
On Jan 8, 2008, at 2:47AM , Laurent Gautier wrote:
> Crashes with unicode labels in plots was reported as a problem
> with R-2.3 to R-2.5.
> It appears fixed with th
Oh, thank goodness. I'm glad it was an easy fix. :-D
-G
On Jan 7, 2008, at 3:01PM , Mario Beauchamp wrote:
> Hi Gregory,
>
> On Jan 7, 2008 10:16 AM, Gregory Warnes <[EMAIL PROTECTED]>
> wrote:
>>
>> Hi Mario,
>>
>>> I had stepped through rpy
On Jan 7, 2008, at 11:32AM , Barry Rowlingson wrote:
> Gregory Warnes wrote:
>>> Thanks for the help, not sure where to go now except maybe if
>>> rpy had an option to pass --no-Rconsole to R on startup...
>> Rpy can pass anything we want to R, but as far as I can
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
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
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
Hi Mario,
> I had stepped through rpy.py in pythonwin and everything was normal.
> It crashes pythonwin in the exec("import _rpy%s as _rpy" % RVER)
> statement, and RVER
> is the right one.
>
Oh dear.
> I will investigate further tomorrow, when I'm on my XP box.
>
Ok, thanks.
-G
> cheers
>
> in touch with him to know what is in there ?
>
> Laurent
>
>
> 2008/1/3, Gregory Warnes <[EMAIL PROTECTED]>:
>>
>> Hi Laurent,
>>
>> I'm glad to see your contributions. Robj, in particular, has needed
>> to be expanded to support all of th
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