G'day rkeshvardoost,

You have some questionable code here. Consider these two adjacent lines:

package R;
package R::startR;
[download]

Are you missing some code that should come after package R;? If not, why did you use package R; in the first place?

The use lib 'R'; line seems to be in the wrong place in your code. Without knowing your directory structure, I can't even say if it's correct (regardless of its position).

In this part of your code:

package R::startR;
...
@EXPORT_OK = qw(startR ...
[download]

that refers to R::startR::startR. Was that what you meant? If so, you haven't declared it!

At this point, I'm starting to have to make many guesses as to your actual intent. The following is how I might have written something that may be close to what you want.

Firstly, I created a directory (pm_1152700_libs) and populated it like this:

$ cat pm_1152700_libs/R.pm
package R;
use Exporter 'import';
our @EXPORT_OK = qw{startR};
sub startR { print 'This is &R::startR' }
1;
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$ cat pm_1152700_libs/R/startR.pm
package R::startR;
use Exporter 'import';
our @EXPORT_OK = qw{startR};
sub startR { print 'This is &R::startR::startR' }
1;
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I then wrote this test script (but do see the notes I've written afterwards):

#!/usr/bin/env perl -l

use strict;
use warnings;

use lib 'pm_1152700_libs';

use R qw{startR};
use R::startR qw{startR};

R::startR();
R::startR::startR();
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which outputs

This is &R::startR
This is &R::startR::startR
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You've used startR in both module and subroutine names. This is highly error-prone and I'd recommend you think of better names.

I've repeated the use of startR in both module and subroutine names; however, note the following:

• To disambiguate the calls to the two &startR routines, I've needed to use fully qualified names, i.e. R::startR() and R::startR::startR().
• If you are going to use fully qualified names, there's little point in adding those identical symbols to your import lists (or even to @EXPORT_OK).
• With better names, the last few lines of my test script could look more like this:

  use R qw{some_startR};
  use R::startR qw{other_startR};
  
  some_startR();
  other_startR();
  [download]

Finally, I strongly advise that you use the strict and warnings pragmata at the start of all your scripts.

Thank you for your response Ken.

To clarify: Since the original code had this error, I tried (almost blindly) anything I could find online to address the error. The original code is the following:

  


sub pick_wavelets {

    `touch $SU_DIR/$file_1.picks`;
    `rm $SU_DIR/$file_1.picks`;
    `sugain agc=1 wagc=0.01 < $SU_DIR/$file_1.su | suxwigb mpicks=$SU_
+DIR/$file_1.picks`;

        }

BEGIN {
  unshift @INC, "/usr/local/perl5.16.0/lib/site_perl/5.16.0/Statistics
+/";
  unshift @INC, "/usr/local/perl5.16.0/lib/site_perl/5.16.0/"; 
 };
use R;
sub setup_R {
        use lib "/usr/lib64/R/";
    use lib "/usr/local/src/RSPerl/src/";
    use R;
    use RReferences; 
    &R::startR("--silent");
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I also tried to define the subroutine by replacing the last part of the code with the following

sub setup_R {
        use lib "/usr/lib64/R/";
    use lib "/usr/local/src/RSPerl/src/";
    use R;
    use RReferences;

        use R qw{startR};
    R::startR();

        &R::startR("--silent");
[download]

However, it still has the same problem. The reason I have not used strict at the beginning is that it makes my program to have more errors. Thank you very much again,

Ru

You don't show the call to setup_R but, from the code you've posted, I get the impression that you're expecting those various use statements to occur at that time. They don't! They occur at compile time. See:

• use - load in a module at compile time
• lib - manipulate @INC at compile time

Perhaps require would be a better choice. See:

• require - load in external functions from a library at runtime

"The reason I have not used strict at the beginning is that it makes my program to have more errors."

Sorry, but that's completely incorrect. strict only reports problems; it doesn't create them.

— Ken

I assume that you downloaded RSPerl from here https://github.com/sboehringer/RSPerl since it has been updated to work with modern versions of Perl.

I have never installed or even tried to install RSPerl but given your problems I thought you might not have seen the documentation. The (old) RSPerl main page has some information on how to install it and use it from Perl. The Calling R From Perl page is probably what you need to read though. It has more detailed information on installation, run-time configuration and usage from within Perl. After reading this, it sounds you didn't run the RSPerl.csh or RSPerl.bsh script (as appropriate) that sets up your environment to find RSPerl.

Oh! I almost forgot. Be sure to read the FAQ because it tells you how to install the modules alongside the rest of the Perl modules instead of in a separate location which should make things easier for you in the long run.