Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-12-11 Thread Laurent Gautier
On 2012-12-11 18:24, Thomas Kluyver wrote: > On 11 December 2012 17:07, Laurent Gautier > wrote: > > I was bugfixing 2.3.0, and since at it I implemented the suggested > changes to the default (dev) branch. That's completely untested; > someone should try. >

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-12-11 Thread Thomas Kluyver
On 11 December 2012 17:07, Laurent Gautier wrote: > I was bugfixing 2.3.0, and since at it I implemented the suggested > changes to the default (dev) branch. That's completely untested; someone > should try. Just looking at the code, I doubt it will work: rp = (p.stdin, p.stdout, p.stderr) ..

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-12-11 Thread Laurent Gautier
On 2012-12-11 15:33, Laurent Gautier wrote: On 2012-12-11 10:27, Yuanda Zhu wrote: Hi, I have a similar problem. After taking all the suggestions from Bitbucket on installing rpy2 under win7 with python 3.2. I installed RTools, defined RHOME, R_HOME, and R_USER and appended the path of R.dll.

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-12-11 Thread Laurent Gautier
On 2012-12-11 10:27, Yuanda Zhu wrote: Hi, I have a similar problem. After taking all the suggestions from Bitbucket on installing rpy2 under win7 with python 3.2. I installed RTools, defined RHOME, R_HOME, and R_USER and appended the path of R.dll. In the end, when running "python setup.py in

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-12-11 Thread Yuanda Zhu
Hi, I have a similar problem. After taking all the suggestions from Bitbucket on installing rpy2 under win7 with python 3.2. I installed RTools, defined RHOME, R_HOME, and R_USER and appended the path of R.dll. In the end, when running "python setup.py install", it it turned out to be following:

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-11-12 Thread Faber Castell
Hi Shane, Thanks for your reply, I looked into PypeR but I will not be able to make it work on my PC. I also looked into pyRserve which is a working alternative to RPy2. However, I would rather use RPy2 which seems to better suit my needs according to this SO thread : http://stackoverflow.com/quest

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-11-12 Thread Shane Carey
Hi, I started to use a module called PypeR and it works good for me. Cheers On Mon, Nov 12, 2012 at 10:27 AM, Faber Castell < fabercastellsince1...@gmail.com> wrote: > Hi, > > I am struggling setting up RPy2 with Windows. > > My config: Win7 32 bit *without admin right* (I understood they are

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-11-12 Thread Faber Castell
Hi, I am struggling setting up RPy2 with Windows. My config: Win7 32 bit *without admin right* (I understood they are not required, am I wrong?) - R 14.2 (C:\R\R-2.14.2\bin\i386\R.exe) - Portable Python 2.7 (C:\PortablePython\App\python.exe) - rpy2-2.3.0beta1.tar.gz I cannot modify environment k

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-10-19 Thread Shane Carey
Hi, Thanks for your help, I have now managed to get Rpy2 installed, but now when I run the program. I get the follwoing error: raise RuntimeError("Unable to locate R.dll within C:\PROGRA~1\R") My R_HOME is this "C:/PROGRA~1/R/R-215~1.0" but I dont know where to change it. Thanks for the help, i

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-10-18 Thread Laurent Gautier
Did you check the following ? https://bitbucket.org/lgautier/rpy2/issue/95/automagic-settings-for-windows On 2012-10-18 17:34, Shane Carey wrote: Already tried that. On Thu, Oct 18, 2012 at 4:33 PM, Paul Hobson > wrote: Add the path to the R executable to your s

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-10-18 Thread Shane Carey
Already tried that. On Thu, Oct 18, 2012 at 4:33 PM, Paul Hobson wrote: > Add the path to the R executable to your system path. > > See here for instructions: > http://www.computerhope.com/issues/ch000549.htm#0 > > On Thu, Oct 18, 2012 at 7:57 AM, Shane Carey wrote: > > Hi, > > > > I have downl

Re: [Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-10-18 Thread Paul Hobson
Add the path to the R executable to your system path. See here for instructions: http://www.computerhope.com/issues/ch000549.htm#0 On Thu, Oct 18, 2012 at 7:57 AM, Shane Carey wrote: > Hi, > > I have downloaded Rpy2, but when I go to install it, I get the following > error, > Error Tried to gues

[Rpy] Error Tried to guess R's HOME but no R command in the PATH

2012-10-18 Thread Shane Carey
Hi, I have downloaded Rpy2, but when I go to install it, I get the following error, Error Tried to guess R's HOME but no R command in the PATH Any idea about this? Many thanks for your help. Cheers -- Shane -- Everyone ha

Re: [Rpy] error message when installing rpy

2012-07-09 Thread Peter Cock
On Tue, Jun 26, 2012 at 9:51 PM, Robert Chase wrote: > Hello, > > An old version of some software needs rpy to function. We tried using > rpy2.classic_rpy and it didn't work. I'm getting the following error message > when I try to install rpy. > >> ls > > ChangeLog examplesMANIFEST.in RE

Re: [Rpy] Error installing rpy2 on mac os x 10.6.8

2012-06-28 Thread Yair Benita
Hi Laurent, Thanks for the info. I will investigate it further and report. My apologies for dropping the list - I didn't realize I did that. Back online now. Best, Yair On Jun 28, 2012, at 5:10 PM, Laurent Gautier wrote: > On 2012-06-28 21:20, Yair Benita wrote: >> Hi Laurent, >> Thanks for th

Re: [Rpy] Error installing rpy2 on mac os x 10.6.8

2012-06-28 Thread Laurent Gautier
On 2012-06-28 07:21, Yair Benita wrote: > Hi All, > I am trying to install rpy2 (2.2.6) on mac os x 10.6.8 with python 2.7 and R > 2.14.1. > I think all my env variables are correct but I still get the underlying > error. I think I previously solved it by forcing it to compile with arch > x86_

[Rpy] Error installing rpy2 on mac os x 10.6.8

2012-06-27 Thread Yair Benita
Hi All, I am trying to install rpy2 (2.2.6) on mac os x 10.6.8 with python 2.7 and R 2.14.1. I think all my env variables are correct but I still get the underlying error. I think I previously solved it by forcing it to compile with arch x86_64 - but I can't remember what I did. Can anyone help?

[Rpy] error message when installing rpy

2012-06-26 Thread Robert Chase
Hello, An old version of some software needs rpy to function. We tried using rpy2.classic_rpy and it didn't work. I'm getting the following error message when I try to install rpy. > ls ChangeLog examplesMANIFEST.in README rpy.py rpy_version.py src debian INSTALL.UNIX

[Rpy] Error reading spss file with RPy

2012-02-17 Thread Marko Limbek
Hi everyone I have resolved the downer problem, but now I have a new problem. There is a need to read a spss base with slavic characters (ČŠŽ) everything works fine. In R everything works fine. Now R code is moved into Python and everything should be fine again, but now slavic characters are not

Re: [Rpy] RPy error

2012-02-07 Thread Peter Cock
On Tue, Feb 7, 2012 at 4:18 PM, Marko Limbek wrote: > I get this > >> R --version > Error: object 'R' not found I meant at the (Windows) terminal try that command, not inside Python. > RPy version is rpy-1.0.3.win32-py2.7-R.2.12.1 and now I have both > R-2.9.0 and R-2.12.1 and both Python 26 and

Re: [Rpy] RPy error

2012-02-07 Thread Marko Limbek
I get this > R --version Error: object 'R' not found RPy version is rpy-1.0.3.win32-py2.7-R.2.12.1 and now I have both R-2.9.0 and R-2.12.1 and both Python 26 and Python 27. Is there a problem with rpy version? Marko On Tue, Feb 7, 2012 at 5:08 PM, Peter Cock wrote: > On Tue, Feb 7, 2012 at

Re: [Rpy] RPy error

2012-02-07 Thread Peter Cock
On Tue, Feb 7, 2012 at 2:23 PM, Marko Limbek wrote: > Hi! > > I get this error. I recently updated SPSS19 to SPS20 and I also have > updated the RPy architecture (python27, pywin, numpy, rpy, r2121) to > be suitable for SPSS20. > Now something is wrong. Perhaps someone knows, what would be the pro

[Rpy] RPy error

2012-02-07 Thread Marko Limbek
Hi! I get this error. I recently updated SPSS19 to SPS20 and I also have updated the RPy architecture (python27, pywin, numpy, rpy, r2121) to be suitable for SPSS20. Now something is wrong. Perhaps someone knows, what would be the problem? Thank you, Marko Traceback (most recent call last): F

Re: [Rpy] Error when I try to install Rpy2 on Centos x64 6.0

2011-11-16 Thread Laurent Gautier
As it says in console output (and in the documentation for rpy2): R was not built as a library http://rpy.sourceforge.net/rpy2/doc-2.2/html/overview.html#requirements L. On 2011-11-15 14:26, Arvind IK Chari wrote: Hi I am trying to install Rpy2 on a centos 6 -x64 system. However I am gettin

[Rpy] Error when I try to install Rpy2 on Centos x64 6.0

2011-11-15 Thread Arvind IK Chari
Hi I am trying to install Rpy2 on a centos 6 -x64 system. However I am getting an error- the full log of error is given below-- [root@localhost rpy2-2.2.3]# python setup.py install running install running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/l

Re: [Rpy] error in python not load rpy, rpy2

2010-09-01 Thread Peter
On Wed, Sep 1, 2010 at 4:22 PM, Ricardo Rodríguez wrote: > hi, again using Rpy and Rpy2, this error is due, > > Error in .Call("R_isMethodsDispatchOn", onOff, PACKAGE = "base") : >   Incorrect number of arguments (2), expecting 1 for R_isMethodsDispatchOn > Error in function (x, pos = -1, envir =

[Rpy] error in python not load rpy, rpy2

2010-09-01 Thread Ricardo Rodríguez
hi, again using Rpy and Rpy2, this error is due, Error in .Call("R_isMethodsDispatchOn", onOff, PACKAGE = "base") : Incorrect number of arguments (2), expecting 1 for R_isMethodsDispatchOn Error in function (x, pos = -1, envir = as.environment(pos), mode = "any", : object 'help' not found jus

Re: [Rpy] error

2010-08-10 Thread Andrew Walsh
Thanks Laurent. I have installed a VMWare Ubuntu machine and am quite impressed. Python runs much faster as a Linux VM under Win7 than it did on a dual boot XP (quad core I7). However I have been having no end of problems trying to get rpy2 to run. When I run the tests python -m 'rpy2tests' I get

Re: [Rpy] error

2010-08-07 Thread Laurent Gautier
Not necessarily. rpy2-2.0.8 can mostly do what you like, however may be not as simply / optimally as the rpy2-2.1.x series could. My recommendation would be to go for the 2.1.x series, or the 2.2.0-dev series if you are of the adventurous kind. There is also more documentation for those, more e

Re: [Rpy] error

2010-08-07 Thread Andrew Walsh
Yes thanks Laurent. So if I want to use factoran from R stats package I presume this means my only option is to install Linux somewhere rather than use windows (if I want to use it from Rpy2 which I do). Andrew. On Sat, Aug 7, 2010 at 9:38 PM, Laurent Gautier wrote: > So we'll all assume that yo

Re: [Rpy] error

2010-08-07 Thread Laurent Gautier
So we'll all assume that you both found out that: - rpy2.robjects.packages only exists for rpy2 >= 2.1.0 - the windows binaries are currently stuck in the past, 2.0.8 being the latest version available. On 8/7/10 12:05 PM, Andrew Walsh wrote: > Huge apologies everyone. I thought I looked thro

Re: [Rpy] error

2010-08-07 Thread Andrew Walsh
Huge apologies everyone. I thought I looked through the list but obviously not very well at all. On Sat, Aug 7, 2010 at 8:03 PM, Andrew Walsh wrote: > I have installed Rpy2 v 2.08 under Windows XP 32. I want to do a > factor analysis from the R stats package. > From the RPY2 documentation I need

[Rpy] error

2010-08-07 Thread Andrew Walsh
I have installed Rpy2 v 2.08 under Windows XP 32. I want to do a factor analysis from the R stats package. >From the RPY2 documentation I need to import rpy2 packages. I find I can import rpy2 and rpy2.objects but rpy2.robjects.packages cannot be found. >>> import rpy2 >>> import rpy2.robjects >>

Re: [Rpy] Error when installing Rpy2

2010-07-06 Thread Fong Chun Chan
For those who have the same problem, I forgot to compiling R from source with --enable-R-shlib to make it a shared library. So try ./configure --enable-R-shlib Hope that helps anyone with that issue. Fong On Tue, Jul 6, 2010 at 1:57 PM, Fong Chun Chan wrote: > I get this: > > > "R was not bui

Re: [Rpy] Error when installing Rpy2

2010-07-06 Thread Fong Chun Chan
I get this: "R was not built as a library" Fong On Tue, Jul 6, 2010 at 1:56 PM, Peter wrote: > On Tue, Jul 6, 2010 at 9:48 PM, Fong Chun Chan > wrote: > >> Hi, > >> > >> I am trying to get Rpy2 installed on my machine, and I downloaded and > ran > >> this command: python setup.py install --pr

Re: [Rpy] Error when installing Rpy2

2010-07-06 Thread Peter
On Tue, Jul 6, 2010 at 9:48 PM, Fong Chun Chan wrote: >> Hi, >> >> I am trying to get Rpy2 installed on my machine, and I downloaded and ran >> this command: python setup.py install --prefix='/home/fong'.  But I've run >> into all these errors (listed below).  Does anyone have any idea on what is

Re: [Rpy] Error when installing Rpy2

2010-07-06 Thread Fong Chun Chan
> > Hi, > > I am trying to get Rpy2 installed on my machine, and I downloaded and ran > this command: python setup.py install --prefix='/home/fong'. But I've run > into all these errors (listed below). Does anyone have any idea on what is > going on? > > Thanks, > > Fong > > > > running

Re: [Rpy] Error: is.atomic(y) is not TRUE

2010-04-26 Thread Mark Larsen
> > Apolagize if this is a stupid question. When I run the following script > > import rpy2.robjects as robjects > x=[5.05,6.75,3.21,2.65] > y=[1.65,2.64,2.64,6.95] > print robjects.r.cor(x,y,method="spearman") > > rpy2 is a lot more careful with automatic conversions. Try: robjects.r.cor(rob

[Rpy] Error: is.atomic(y) is not TRUE

2010-04-26 Thread António Saragga Seabra
Hi all, Apolagize if this is a stupid question. When I run the following script import rpy2.robjects as robjects x=[5.05,6.75,3.21,2.65] y=[1.65,2.64,2.64,6.95] print robjects.r.cor(x,y,method="spearman") get the following message Traceback (most recent call last): File "C:\Python26\Lib\site

Re: [Rpy] error on importing rpy2.objects

2010-02-05 Thread Laurent Gautier
On 2/5/10 8:01 PM, Mike Dewar wrote: > Hi, > > I'm not sure exactly what's changed since rpy2 was working. Quite > possibly both the python and the R versions have changed. Yes I've > tried re-installing rpy2, both via easy_install and by downloading > the latest version and running python setup.p

Re: [Rpy] error on importing rpy2.objects

2010-02-05 Thread Mike Dewar
Hi, I'm not sure exactly what's changed since rpy2 was working. Quite possibly both the python and the R versions have changed. Yes I've tried re-installing rpy2, both via easy_install and by downloading the latest version and running python setup.py install. The version of R I'm using could b

Re: [Rpy] error on importing rpy2.objects

2010-02-05 Thread Laurent Gautier
On 2/5/10 6:56 PM, Mike Dewar wrote: > Hi, > > I'm getting a weird error when trying to import rpy2.robjects. I'm on > Mac OS X, 10.6.2. I haven't used rpy2 for a while, but I'm sure that > last time I did use it, this error was not occurring. I have no idea > what's changed, nor any real ability t

[Rpy] error on importing rpy2.objects

2010-02-05 Thread Mike Dewar
Hi, I'm getting a weird error when trying to import rpy2.robjects. I'm on Mac OS X, 10.6.2. I haven't used rpy2 for a while, but I'm sure that last time I did use it, this error was not occurring. I have no idea what's changed, nor any real ability to track down the source of this error. Here'

Re: [Rpy] Error using rpy2

2009-12-08 Thread Laurent Gautier
The error message refers to undefined symbols in shared C libraries for R recommended packages, not about whether can be found or written into. Did you reinstall rpy2 after the more recent R was installed ? L. On 12/8/09 1:15 PM, B.A.D.C.M.D Santos wrote: > I managed to ask our Systems Admin

[Rpy] Error using rpy2

2009-12-08 Thread B.A.D.C.M.D Santos
I managed to ask our Systems Administrator to install a new version of R. I know have R2.10.0 installed but rpy2 is still not very happy with it. When I try to import robjects I get the following errors: Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2 Type "help", "copyri

Re: [Rpy] Error using rpy2

2009-12-07 Thread Laurent Gautier
rpy2 will be happier with R >= 2.8 (as bugs in R were fixed) L. On 12/7/09 12:33 PM, B.A.D.C.M.D Santos wrote: > The problem is that I get the error when import robjects. When I tried > to replicate your instructions I got the following error: In [5]: > print(rpy2.robjects.r['search']()) > --

[Rpy] Error using rpy2

2009-12-07 Thread B.A.D.C.M.D Santos
The problem is that I get the error when import robjects. When I tried to replicate your instructions I got the following error: In [5]: print(rpy2.robjects.r['search']()) --- AttributeError Traceback (most recent call last

Re: [Rpy] Error using rpy2

2009-12-07 Thread Laurent Gautier
phyper is part of "stats", which should be loaded by defaults. Check what returns: print(robjects.r["search"]()) If not attached, you'll have to load it. L. PS: The R version, Python version, and rpy2 version is generally a good thing to tell us. On 12/7/09 11:06 AM, B.A.D.C.M.D Santos wrot

[Rpy] Error using rpy2

2009-12-07 Thread B.A.D.C.M.D Santos
I am getting an error when using rpy2 under a Debian operating system. It seems to be some kind of problem with R_LIBS enviromental variable but I cannot get it completly. Can someone please explain me better the problem so I can try to fix. I have tried to export a varible R_LIBS but the probl

[Rpy] Error using barplot with rpy2

2009-11-25 Thread B.A.D.C.M.D Santos
I am trying to use barplot but everytime I try to pass a list as an argument I get the following error: [code] >>> barplot([1]) Traceback (most recent call last): File "", line 1, in File "C:\Python26\lib\site-packages\rpy2\robjects\__init__.py", line 423, in __call__ res = super(RFuncti

Re: [Rpy] Error using phyper with rpy2

2009-11-23 Thread Laurent Gautier
Peter wrote: > On Mon, Nov 23, 2009 at 1:57 PM, B.A.D.C.M.D Santos wrote: >> This is probably just a stupid problem but for some reason I can't find a >> solution anywhere. >> >> I am trying to use phyper from R using rpy2. The problem is that when I try >> to run the following code: [code] self.p

Re: [Rpy] Error using phyper with rpy2

2009-11-23 Thread Peter
On Mon, Nov 23, 2009 at 1:57 PM, B.A.D.C.M.D Santos wrote: > > This is probably just a stupid problem but for some reason I can't find a > solution anywhere. > > I am trying to use phyper from R using rpy2. The problem is that when I try > to run the following code: [code] self.phyper = robjects.r

[Rpy] Error using phyper with rpy2

2009-11-23 Thread B.A.D.C.M.D Santos
This is probably just a stupid problem but for some reason I can't find a solution anywhere. I am trying to use phyper from R using rpy2. The problem is that when I try to run the following code: [code] self.phyper = robjects.r('phyper') ' ' ' nPvalue=1-self.phyper(k,21,440,n,lower_tail=False)[

Re: [Rpy] Error loading bioconductor affy library..

2009-09-11 Thread Laurent Gautier
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(

[Rpy] Error loading bioconductor affy library..

2009-09-11 Thread Paul Geeleher
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 Bi

[Rpy] Error: variables ... were specified with different types from the fit

2009-04-02 Thread Ed Rahn
I get the following error: rpy.RPy_RException: Error: variables ‘X3’, ‘X13’, ‘X29’, ‘X30’, ‘X33’, ‘X35’, ‘X36’, ‘X37’, ‘X43’, ‘X45’, ‘X50’, ‘X65’, ‘X66’, ‘X67’, ‘X68’, ‘X70’, ‘X71’, ‘X72’, ‘X73’, ‘X209’, ‘X210’, ‘X213’, ‘X214’, ‘X215’, ‘X216’, ‘X217’, ‘X223’, ‘X250’ were specified with different

Re: [Rpy] error building rpy-1.0.3 for R 2.8.0

2008-12-16 Thread Paul Hartley
thanks -- I had trouble searching the listserv archives for this workaround -- if this is related to R 2.8.0, perhaps the rpy maintainers could post this workaround to the installation documentation -- seems like it'd be useful for a lot of people still using the 1.0 version. paul On Tue, Dec 16,

Re: [Rpy] error building rpy-1.0.3 for R 2.8.0

2008-12-16 Thread Davide Cittaro
As posted in a previous email On Dec 16, 2008, at 10:45 AM, Paul Hartley wrote: I recently upgraded R to 2.8.0 and built it with -enable-R-shlib. When I tried to re-build rpy 1.0.3, I get the following error, which I assume means something changed in R 2.8.0 that is not accounted for by

[Rpy] error building rpy-1.0.3 for R 2.8.0

2008-12-16 Thread Paul Hartley
I recently upgraded R to 2.8.0 and built it with -enable-R-shlib. When I tried to re-build rpy 1.0.3, I get the following error, which I assume means something changed in R 2.8.0 that is not accounted for by rpy 1.0.3. I tried rpy 1.0.2 and got the same error. I have never had a previous issue r

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

2008-04-10 Thread Gregory Warnes
Ok, it looks like some code inserted to prevent issues on Win32, incorrectly disabled the changes everywhere. I've just submitted a change to SVN that should resolve this issue. I'll test it on OSX and Win32 and, if all goes well, release a new version with this correction. -G On Ap

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

2008-04-10 Thread Gregory Warnes
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 to the limit

2008-04-09 Thread Laurent Gautier
I can reproduce it with python-2.5 / R-2.6.1 as well. The error might well only have to do with X11 devices only, so I wanted to try R-2.7.0 (since it will/should be using cairo devices by default), but no luck: I already get error a RunTime error at load time :-/ . On the other end, I managed to

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

2008-04-09 Thread A_Berger
I've been experiencing this error with several versions of rpy. The only version that did work properly was Rpy1RC3, however newer versions of R require newer versions of Rpy, and I had to update to a newer Rpy and survive with the error. I've heard that this issue only arises on *nix systems

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

2008-04-09 Thread Lukasz Szybalski
On Wed, Apr 9, 2008 at 3:26 AM, Laurent Gautier <[EMAIL PROTECTED]> wrote: > Issues with the C stack are encountered now and then, and this might > be a problem > with R: > http://tolstoy.newcastle.edu.au/R/e4/help/08/01/2069.html > > More generally, whenever the host application (here the Pyth

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

2008-04-09 Thread Laurent Gautier
Issues with the C stack are encountered now and then, and this might be a problem with R: http://tolstoy.newcastle.edu.au/R/e4/help/08/01/2069.html More generally, whenever the host application (here the Python process) is manipulating the stack (like when using threads I think) the problem might

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

2008-04-09 Thread Daniel Dvorkin
I get these sorts of memory errors (sometimes a segfault, sometimes a bus error) too, a fair amount, when plotting in RPy. Nothing else, just plotting. I don't have any idea what's going on either, but I'd sure like to know how to stop it from happening. ---

[Rpy] Error during wrapup: C stack usage is too close to the limit

2008-04-08 Thread Lucas Szybalski
I was trying to refresh my memory and see how things are going in rpy, but: >>> from rpy import * >>> x = range(1,11) >>> y = [i**2 for i in x] >>> z = [i**3 for i in x] >>> r.plot(x, y, main='My second plot', xlab='x', ylab='y', type='l', col='blue') >>> r.lines(x, z, col='red') >>> Error

Re: [Rpy] error reading Rconsole

2008-01-07 Thread Gregory Warnes
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 tell R >> itself doesn't ha

Re: [Rpy] error reading Rconsole

2008-01-03 Thread Gregory Warnes
Hi Barry, Grab the latest SVN version of rpy. I've added the ability to avoid setting up reading and writing the console via rpy_options: import rpy_options rpy_options.set_options(SETUP_READ_CONSOLE=False, SETUP_WRITE_CONSOLE=False, SETUP_SHOWFILES=False) from rpy im

Re: [Rpy] error reading Rconsole

2008-01-02 Thread Barry Rowlingson
Gregory Warnes wrote: > Hi Barry, > This will prevent R/Rpy from being able to ready *anything* from the > console, so be careful. If this works, then you should find out how > QGIS sets up Python's console read operation and do the same thing > for R/Rpy. Righto, I'll try that later to

Re: [Rpy] error reading Rconsole

2008-01-02 Thread Gregory Warnes
Hi Barry, I suspect the problem is that QGIS has set up python's console input differently than rpy expects. At the moment, there is no way to tell RPy to do something different with i/o during startup. (After startup you can call set_rpy_output() and set_rpy_input() to provide new i/o

[Rpy] error reading Rconsole

2008-01-02 Thread Barry Rowlingson
Starting with a fresh Windows XP system I've installed R 2.6.1 and the latest Rpy and Python 2.5 from binaries. That all works fine together. I've also installed Quantum GIS (QGIS) 0.9.1 from released binaries. QGIS has an embedded python interpreter which gives access to the geographic data an

Re: [Rpy] error in building rpy in linux power-pc[sec=unclassified]

2007-06-23 Thread Gregory Warnes
Hello Mohar, This question is outside of the RPy scope. It looks like the type of question that should be posed to the R-devel mailing list: [EMAIL PROTECTED] -Greg On Jun 20, 2007, at 8:25PM , Mohar Chattopadhyay wrote: Dear all, I have encountered errors in compiling R-2.5.0

[Rpy] error in building rpy in linux power-pc[sec=unclassified]

2007-06-22 Thread Mohar Chattopadhyay
Dear all, I have encountered errors in compiling R-2.5.0 and R-2.4.0 in a linux machine (power-pc). I can successfully build it from the source code if I do not use the '--enable-R-shlib' option while executing the './configure' command as mentioned in rpy documentation. Using the `--enable-R-shl