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Calling the program "R" from within a perl script fails in Windows

BarryHall
Novice

Jun 18, 2010, 11:24 AM

Post #1 of 11 (882 views)

Calling the program "R" from within a perl script fails in Windows	Can't Post

I need to call the program "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

FishMonger
Veteran

Jun 18, 2010, 12:30 PM

Post #2 of 11 (879 views)

Re: [BarryHall] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

Try changing:

Code

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

To:

Code

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

BarryHall
Novice

Jun 18, 2010, 12:45 PM

Post #3 of 11 (876 views)

Re: [FishMonger] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

Thanks for trying, but the change made no difference at all. The behavior remains identical
Barry Hall

FishMonger
Veteran

Jun 18, 2010, 12:50 PM

Post #4 of 11 (874 views)

Re: [BarryHall] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

Check your $ENV{PATH} setting to see if it includes the directory to "R". If it doesn't, then either adjust that var or include the full path in the system call.

BarryHall
Novice

Jun 18, 2010, 4:36 PM

Post #5 of 11 (864 views)

Re: [FishMonger] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

The path environment variable does contain the path to R.

FishMonger
Veteran

Jun 18, 2010, 4:38 PM

Post #6 of 11 (863 views)

Re: [BarryHall] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

Then the answer is clear. You need to append it to that hash value.

BarryHall
Novice

Jun 18, 2010, 5:01 PM

Post #7 of 11 (860 views)

Re: [FishMonger] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

Many thanks. I modified the code to read
my $R = "C:\\Program Files\\R\\R-2.11.1\\bin\\R";
my @args = ("$R","--vanilla", "--quiet", "--file=Rblock");

It now works just fine.

The only issue is that other users may install different versions of R or install it elsewhere. I think I will need to have my perl script search for the location of R.exe, use getcwd() to get the path to that folder, then use that to set the value of $R.

FishMonger
Veteran

Jun 18, 2010, 5:15 PM

Post #8 of 11 (859 views)

Re: [BarryHall] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

A better option would be to store the path in a config file and have the script read that config file.

BarryHall
Novice

Jun 18, 2010, 10:07 PM

Post #9 of 11 (854 views)

Re: [FishMonger] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

Aha! Yes, I see how that would be a better option. Thank you.
BGH

shawnhcorey
Enthusiast

Jun 19, 2010, 4:38 AM

Post #10 of 11 (844 views)

Re: [FishMonger] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

In Reply To

Try changing:

Code

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

To:

Code

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

Don't you mean?

Code

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

__END__

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FishMonger
Veteran

Jun 19, 2010, 5:05 AM

Post #11 of 11 (841 views)

Re: [shawnhcorey] Calling the program "R" from within a perl script fails in Windows [In reply to]	Can't Post

In Reply To

Try changing:

Code

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

To:

Code

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

Don't you mean?

Code

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

Yes, that is what I meant. Thanks for catching my error

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