in reply to site_perl files

Can somebody please explain me what should be in the folder perl5.10/lib/site_perl/?

When one builds and installs perl from source, site_perl will be empty (if it even exists).
Any non-core modules that the user subsequently installs will go into site_perl (creating that directory in the process if needs be).
With the system perl, it's recommended that additional modules be installed using the system's package manager. I don't know if the system's package manager will put those additional modules into site_perl.

I'm not aware of any package that should require the presence of site_perl. site_perl should just be one of a number of locations that are searched when a module is to be loaded - and it doesn't matter to perl which one of those (@INC) directories contain the module, so long as least one of them does.
And it doesn't matter to perl if one or more of those directories don't exist.
If the module exists in multiple @INC directories perl will load the one that it finds first.

Cheers,
Rob

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Re^2: site_perl files
by yaklichk0719 (Acolyte) on Jul 20, 2018 at 14:37 UTC
    Dear Rob, Thank you so much for your reply. Basically, I have been trying to run a WBSA package written in Java, but it integrates Perl libraries for genomic analysis and in bash_profile the followings written (author version): export PERL5LIB=/software/R-2.15.3/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi:/software/perl5.10/lib/5.10.1:/software/perl5.10/lib/site_perl: At this point we have not been unable to start the package working correctly but I have been trying to. It was originality tested on CentOS 6.3 with Perl 5.10. We have CentOS 7 with Perl version 5.16. I wanna stay with the original paths written in bash_profile but I was unable to find the folder: site_Perl.
[reply]

      yaklichk0719:

      It appears from the PERL5LIB variable that it's expecting you to be using RSPerl. Have you installed that? It may provide the missing piece(s) you're looking for. I did a quick search and found it at http://www.omegahat.net/RSPerl.

      Update: fixed link to RSPerl (missing slashes)

      ...roboticus

      When your only tool is a hammer, all problems look like your thumb.

[reply]
        I tried to installed RSPerl but I am getting. I put the compressed file in /software/R-2.15.3/library and tried to install using the command: R CMD INSTALL RSPerl_0.92-1.tar.gz

        I am getting an error: 

        Converters.c: At top level:
Converters.c:1037: error: expected ‘)’ before ‘*’ token
Converters.c:1078: error: expected ‘)’ before ‘*’ token
make: *** [Converters.o] Error 1
ERROR: compilation failed for package ‘RSPerl’
* removing ‘/usr/local/lib64/R/library/RSPerl’

        [download]
        I wonder what the problem could be? Should I re-install R?

        2018-07-25 Athanasius added code and paragraph tags

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