Evaluating Entire Matlab code at a time - R-help

Fri, Dec 29, 2006 11:47 PM #

Hi.

On 12/30/06, Bhanu Kalyan.K <kalyansikha at yahoo.com> wrote:

Dear Mr.Bengtsson,

The steps you have suggested are working for single lines of matlab
statements. But, as i mentioned earlier, If i want to see the output of an
entire matlab code (say swissroll.m) then you suggested me to do
res <- evaluate(matlab, "swissroll").
When i did this the output looks something like:

res <- evaluate(matlab, "swissroll")

 Sending expression on the Matlab server to be evaluated...: 'swissroll'
 Received an 'MatlabException' reply (-1) from the Matlab server: 'Undefined
function or variable 'lle'.'
 Error in list("evaluate(matlab, "swissroll")" = <environment>,
"evaluate.Matlab(matlab, "swissroll")" = <environment>,  :

 [2006-12-30 11:58:32] Exception: MatlabException: Undefined function or
variable 'lle'.
   at throw(Exception(...))
   at throw.default("MatlabException: ", lasterr)
   at throw("MatlabException: ", lasterr)
   at readResult.Matlab(this)
   at readResult(this)
   at evaluate.Matlab(matlab, "swissroll")
   at evaluate(matlab, "swissroll")

// Here another matlab window titled "Figure no.1" (corresponding to the
actual matlab output of swissroll.m) opened, but the window is blank. No
output is being displayed. However,  when i used the same command for
another matlab code, kMeansCluster.m, the warnings/Exceptions generated are
similar to that os swissroll.m. Here is the output:

res <- evaluate(matlab, "kMeansCluster;")

Sending expression on the Matlab server to be evaluated...: 'kMeansCluster;'
Received an 'MatlabException' reply (-1) from the Matlab server: 'Undefined
function or variable 'kMeansCluster'.'
Error in list("evaluate(matlab, "kMeansCluster;")" = <environment>,
"evaluate.Matlab(matlab, "kMeansCluster;")" = <environment>,  :

[2006-12-30 11:56:34] Exception: MatlabException: Undefined function or
variable 'kMeansCluster'.
  at throw(Exception(...))
  at throw.default("MatlabException: ", lasterr)
  at throw("MatlabException: ", lasterr)
  at readResult.Matlab(this)
  at readResult(this)
  at evaluate.Matlab(matlab, "kMeansCluster;")
  at evaluate(matlab, "kMeansCluster;")

The warnings generated are almost similar for those two different matlab
codes. So i feel that the problem lies with the R and not the code. What do
u suggest? how to deal with this?

To me this looks like Matlab can't find those commands, and then it
has nothing to with R. Make sure your Matlab scripts are available in
the Matlab path or in the working directory of Matlab.  You check the
working directory of Matlab with:

 evaluate(matlab, "pwd=cd();");
 pwd <- getVariable(matlab, "pwd")$pwd;
 print(pwd);

Check to see if your scripts are in the working directory:

 evaluate(matlab, "files=dir();")
 files <- getVariable(matlab, "files")$files
 unlist(files["name",,])

If not, you have to update your Matlab path or change the working directory.

Hope this helps

Henrik

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Bhanu Kalyan.K

Sat, Dec 30, 2006 1:42 AM #

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Henrik Bengtsson

Sat, Dec 30, 2006 1:51 AM #

This is very odd, but maybe 'cd' is not a command on your Windows
Matlab installation.  I tried the same code on a Unix installation (I
don't have access to Matlab for Windows but others have been using
R.matlab there successfully).  Find out what the command for getting
the current directory in your Matlab version is and use that instead.

You could also troubleshoot by this:

1. Start Matlab using Matlab$startServer(minimize=FALSE)
2. Setup the Matlab connection from R and close it with close(matlab).
3. Go to the Matlab windows and try the commands that failed for you
    when called from R. This will give you a hint.

Remember, there is nothing magic going on.  Think about the R Matlab
connection as R is typing the Matlab commands for you; anything you
can do in that Matlab windows which you did close(matlab) on you can
do with evaluate(matlab, ...) - before closing it that is.

/Henrik

On 12/30/06, Bhanu Kalyan.K <kalyansikha at yahoo.com> wrote:

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