perl not found R

Asked Sep 29 '15 at 13:33

Active Sep 29 '15 at 13:51

Viewed 1,722 times

I am trying to call a perl script in R using the system command
This is what I tried:

system("perl R/BEMSER.pl -f R/fasta.txt -m R/matrix.txt -o R/result.txt -tu 100 -tl -100 -c", intern=F)

I get the following error message:

Warning message:
In system("perl R/BEMSER.pl -f R/fasta.txt -m R/matrix.txt -o R/result.txt -tu 100 -tl -100 -c",  :
  perl not found

The command inside the system call works in the command line (giving parameters to the perl script, the files perl should use are in a special folder called "R"), perl is of course installed. What can I do to call the perl script from R?

edited Sep 29 '15 at 13:51

asked Sep 29 '15 at 13:33

MaxS

2

Use the full path to `perl`? – mob Sep 29 '15 at 13:40
install the `gdata` package and see if running `gdata:::findPerl()` comes back with something. alternately, ensure the path to `perl` is in your `PATH`. – hrbrmstr Sep 29 '15 at 13:41
Are you by chance on Windows? – Dirk Eddelbuettel Sep 29 '15 at 13:42
You may type this command on the terminal to find the path to your perl installation's binary, and replace perl with the full path `which perl` – Pradeep Sep 29 '15 at 13:44
@mob If you want to make your script unportable, sure. – Konrad Rudolph Sep 29 '15 at 14:01
I used: system("C:/Strawberry/perl/bin R/BEMSER.pl -f R/fasta.txt -m R/matrix.txt -o R/result.txt -tu 100 -tl -100 -c", intern=F) returning that it does not find C:/Strawberry/perl/bin. gdata can't find perl and yes, I am on windows (7) – MaxS Sep 29 '15 at 15:35
1

Dont you want C:/Strawberry/perl/bin/perl? – stark Sep 29 '15 at 16:57
C:/Strawberry/perl/bin/perl was working. Thanks! – MaxS Oct 01 '15 at 06:47

perl not found R

0 Answers0