Hi,
I am looking for the possibility to call R functions from Matlab.
googling around I found:
http://www.omegahat.org/RMatlab/
The developers say that there's no official Windows or Mac version
yet. nevertheless i tried.
my first attempt was unsuccessful. doing
R CMD INSTALL RMatlab
said that it didn't find libR.so
since I found a libR.dylib in /Library/Frameworks/R.framework/Versions/
2.6/Resources/lib I changed some lines in the configure file in the
RMatlab folder:
#if test -r $R_HOME/lib/libR.so ; then
if test -r $R_HOME/lib/libR.dylib ; then
R_SHARED_LIB_DIR=$R_HOME/lib
#elif test -r $R_HOME/bin/libR.so ; then
elif test -r $R_HOME/bin/libR.dylib ; then
R_SHARED_LIB_DIR=$R_HOME/bin
Installation appears to work, except of some warnings. I attach the
output after R CMD INSTALL RMatlab below.
then I run the shell script:
. /Library/Frameworks/R.framework/Resources/library/RMatlab/scripts/
RMatlab.sh
and set the environments (I did it within Matlab but I don't know if
that's correct; i also tried setting the environment from within the
bash shell using export):
setenv R_HOME /Library/Frameworks/R.framework/Resources
setenv LD_LIBRARY_PATH $R_HOME/lib
when I try to start RMatlab from Matlab, Matlab crashes:
x = initializeR({'Rmatlab'})
In R when starting library(RMatlab) I get error messages:
Error in dyn.load(file, ...) :
kann shared library '/Library/Frameworks/R.framework/Resources/
library/RMatlab/libs/i386/RMatlab.so' nicht laden:
dlopen(/Library/Frameworks/R.framework/Resources/library/RMatlab/
libs/i386/RMatlab.so, 6): Library not loaded: @loader_path/libeng.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/library/
RMatlab/libs/i386/RMatlab.so
Reason: no suitable image found. Did find:
/usr/local/lib/libeng.dylib: stat() failed with errno=62
Fehler: Laden von Paket/Namensraum für 'RMatlab' fehlgeschlagen
As you might have noticed I am not very experienced other than with
binary versions, but I RMatlab.so is probably not suited on OS X. I
considered building a dylib from XCode (following yet another example
found when googling), but I think I was doing nonsense.
So here's the question: has anyone managed to successfully install
RMatlab on OS X? If yes how (perhaps I did some mistake hile
installing)? Or do you know how it would work? any pointers /
instructions appreciated.
btw, I'm working on OS X 10.5.1 and using R v2.6.
best wishes,
nathan
########Output of R CMD INSTALL RMatlab
* Installing to library '/Library/Frameworks/R.framework/Resources/
library'
* Installing *source* package 'RMatlab' ...
checking for mex... /usr/bin/mex
checking for sed... /usr/bin/sed
Looking for mclmcr.h
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
configure: creating ./config.status
config.status: creating inst/scripts/RMatlab.csh
config.status: creating inst/scripts/RMatlab.sh
config.status: creating src/Makefile
Using the following settings
Mex compiler: /usr/bin/mex
Mex extension: mexmaci
Mex linker flags: -Wl,-flat_namespace -undefined suppress
-bundle
R shared library directory: /Library/Frameworks/R.framework/
Resources/lib
Installation directory: /Library/Frameworks/R.framework/
Resources/library/RMatlab
*********************************************************
To set the environment variables to run R from within Matlab
or vice versa, source the relevant shell script into your shell
before running Matlab or R
Bourne or Bash shell:
. /Library/Frameworks/R.framework/Resources/library/RMatlab/
scripts/RMatlab.sh
Csh or Tcsh shell:
source /Library/Frameworks/R.framework/Resources/library/RMatlab/
scripts/RMatlab.csh
*********************************************************
** libs
** arch - i386
/usr/bin/mex -argcheck -I/Library/Frameworks/R.framework/Resources/
include -L/Library/Frameworks/R.framework/Resources/lib -lR callR.c
convert.c
convert.c: In function convertFromRObject:
convert.c:408: warning: assignment discards qualifiers from pointer
target type
ld: warning, duplicate dylib /Applications/MATLAB_R2007b/bin/maci/libz.
1.dylib
/usr/bin/mex -argcheck -I/Library/Frameworks/R.framework/Resources/
include -L/Library/Frameworks/R.framework/Resources/lib -lR
initializeR.c
ld: warning, duplicate dylib /Applications/MATLAB_R2007b/bin/maci/libz.
1.dylib
/usr/bin/mex -argcheck -I/Library/Frameworks/R.framework/Resources/
include -L/Library/Frameworks/R.framework/Resources/lib -lR
callNamedR.c convert.c
convert.c: In function convertFromRObject:
convert.c:408: warning: assignment discards qualifiers from pointer
target type
ld: warning, duplicate dylib /Applications/MATLAB_R2007b/bin/maci/libz.
1.dylib
cp *.mexmaci ../inst/mex
** R
** inst
** help
>>> Building/Updating help pages for package 'RMatlab'
Formats: text html latex example
** building package indices ...
* DONE (RMatlab)
--------------------------------
Dr. Nathan Weisz
INSERM - Unité 821
Dynamique cérébrale et cognition
Centre Hospitalier Le Vinatier, Bâtiment 452
95 Boulevard Pinel
69500 Bron, France
Tel: ++33 - (0)4 - 7213 8915
Email: [EMAIL PROTECTED]
Chat-AV: [EMAIL PROTECTED]
Homepage: http://web.mac.com/nathanweisz
Neurotree: http://neurotree.org/neurotree/tree.php?pid=8692
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
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