R help - Jun 2010 - Problem calling R from within perl script on Windows

I need to call R from within a Perl script.  I do so using a system call like
this:
@args = ('R --vanilla --quiet --file=Rblock'); 
system(@args) == 0 or die "system @args failed: $!";

The script works perfectly when run in Mac OSX or Linux.  In Windows XP it
fails with the message " 'R' is not recognized as an internal or
external
command, operable program or batch file".

To ensure that R was properly installed and that the environment variable
"path" was correctly set, I executed the same command (R --vanilla
--quiet
--file=Rblock) from the command line and it worked perfectly; i.e. R ran
with the expected behavior.

Similar system calls to other external programs, e.g.
@args = ('Notepad'); 
system(@args) == 0 or die "system @args failed: $!";
work perfectly.

Is there any obvious reason that this particular call works from the command
line but not from within a perl script?

Thanks for any assistance
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On Fri, Jun 18, 2010 at 3:11 PM, Barry Hall <barryhall at zeninternet.com>
wrote:
>
> I need to call R from within a Perl script. ?I do so using a system call
like
> this:
> @args = ('R --vanilla --quiet --file=Rblock');
> system(@args) == 0 or die "system @args failed: $!";
>
> The script works perfectly when run in Mac OSX or Linux. ?In Windows XP it
> fails with the message " 'R' is not recognized as an internal
or external
> command, operable program or batch file".
>
> To ensure that R was properly installed and that the environment variable
> "path" was correctly set, I executed the same command (R
--vanilla --quiet
> --file=Rblock) from the command line and it worked perfectly; i.e. R ran
> with the expected behavior.
>
> Similar system calls to other external programs, e.g.
> @args = ('Notepad');
> system(@args) == 0 or die "system @args failed: $!";
> work perfectly.
>
> Is there any obvious reason that this particular call works from the
command
> line but not from within a perl script?
>
That error is coming from the Windows console so you likely have a
PATH problem.  Fix your path or use the absolute path in your program.

Note that unless you told it not to under normal circumstances the R
installer puts a key in the registry and you can alternatively look it
up to find R that way.  A batch file that does that is in the
batchfiles collection at http://batchfiles.googlecode.com

Someone with more Windows and/or Perl experience will be of more use, 
but guessing here:

1) Try calling system with a program that echoes the path, perhaps the 
system command is not using the same path variable as you think.

2) specify the full path to R (using proper escaping of backslashes 
and/or spaces as necessary), and see if that helps at all.


Barry Hall wrote:
> I need to call R from within a Perl script.  I do so using a system call
like
> this:
> @args = ('R --vanilla --quiet --file=Rblock'); 
> system(@args) == 0 or die "system @args failed: $!";
> 
> The script works perfectly when run in Mac OSX or Linux.  In Windows XP it
> fails with the message " 'R' is not recognized as an internal
or external
> command, operable program or batch file".
> 
> To ensure that R was properly installed and that the environment variable
> "path" was correctly set, I executed the same command (R
--vanilla --quiet
> --file=Rblock) from the command line and it worked perfectly; i.e. R ran
> with the expected behavior.
> 
> Similar system calls to other external programs, e.g.
> @args = ('Notepad'); 
> system(@args) == 0 or die "system @args failed: $!";
> work perfectly.
> 
> Is there any obvious reason that this particular call works from the
command
> line but not from within a perl script?
> 
> Thanks for any assistance

Barry Hall wrote:
> 
> I need to call R from within a Perl script.  I do so using a system call
> like this:
> @args = ('R --vanilla --quiet --file=Rblock'); 
> system(@args) == 0 or die "system @args failed: $!";
> 
Try this

@args = ('R', '--vanilla --quiet --file=Rblock'); 

i.e. make @args consist of two items: the first is the command/program you
want to run and the second consists of  the command line arguments you want
to pass to the program.

/Berend
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