I have a .pl script in which starts by:
#!/usr/bin/perl
use XML::XPath;
use Getopt::Long;
I can't seem to run that via perl myScript.pl, having this error:
(#INC contains: /usr/share/ /usr/local/lib64/perl5 /usr/local/share/perl5/usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at most_generic_wrapper.pl line 3.
BEGIN failed--compilation aborted at myScript.pl line 3.
1- I tried to locate the XPath.pm file and export that as:
export PERL5LIB=/usr/share/perl5/XML/Twig
and
export PERL5LIB=/usr/share/perl5/XML
2- Installed perl -MCPAN -e 'install XML::Parser'
3- Used -I to explicitly define the path as:
perl -I perl -MCPAN -e 'install XML::Parser' myScript.pl
4- changing the line 3 to use XML::Twig::XPath; led to:
cannot use XML::Twig::XPath: neither XML::XPathEngine 0.09+ nor XML::XPath are available at /usr/share/perl5/XML/Twig/XPath.pm line 11.
BEGIN failed--compilation aborted at /usr/share/perl5/XML/Twig/XPath.pm line 13.`
But none of them solved the issue and I keep receiving the same error at line.3.
P.S: Running on CentOS 6.2 with the kernel 2.6.32-358 and perl --version=v5.10.1 (*) built for x86_64-linux-thread-multi
Any helps would be appreciated,
Your title says XML::XPath can't be found, but your question indicates you tried to install XML::Parser. Did you try to install XML::XPath?
From man perlrun: "If PERL5LIB is not defined, PERLLIB". You seem to have tried setting PERLIB5 (notice the spelling difference: the var is PERL5LIB (or PERLLIB), not PERLIB5).
From man perlrun: "PERL5LIB -- A list of directories in which to look for Perl library files before looking in the standard library and the current directory." You seem to have tried setting it to the full path to a .pm file, rather than a directory.
The file you assigned would be XML::Twig::XPath, not XML::XPath; those are two different Perl modules.
Edit: After looking at your revised question:
I'm not sure if your script requires XML::Twig::XPath or XML::XPath, or if either one can provide the API you need. However, XML::Twig::XPath seems to depend on XML::XPath so you will need XML::XPath no matter what, and it looks like XML::XPath is not installed on your system. I think that's probably the main problem. Please try to install XML::XPath using CPAN.
The value of the PERL5LIB variable (or the argument to the -I option) should be the directory that sits at the base of the package-qualified module file. For example, if XML::XPath is located at ~/perl_custom_modules/XML/XPath.pm, then you need to set PERL5LIB (or the -I argument) to ~/perl_custom_modules. The XML directory is part of the package qualification of the module, so does not need to be included in the include path.
Related
I was installing repeatsmasker and it apparently seems to work because it shows "Congratulations! RepeatMasker is now ready to use."
But when I run it it reports "Can't locate Text/Soundex.pm...". so I installed the module by "sudo cpan Text::Soundex", and by the end it tells me "Text::Soundex is up to date (3.05)." It seems the module is already installed, but RepeatMasker still has the same problem, as I'll show you in this code:
fragua#picci:~/RM/RepeatMasker$ sudo cpan Text::Soundex
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/fragua/.cpan/Metadata'
Database was generated on Fri, 19 Apr 2019 22:17:03 GMT
Text::Soundex is up to date (3.05).
fragua#picci:~/RM/RepeatMasker$ ./RepeatMasker -s -lib /home/fragua/RepeatScout-1.0.5/ObiINK5k_repeats_filtered1.fasta /home/fragua/Documenti/Workdirectory/ObiINC5k.fa
Can't locate Text/Soundex.pm in #INC (you may need to install the Text::Soundex module) (#INC contains: /home/fragua/RM/RepeatMasker /home/fragua/perl5/lib/perl5 /home/fragua/anaconda/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/fragua/anaconda/lib/site_perl/5.26.2 /home/fragua/anaconda/lib/5.26.2/x86_64-linux-thread-multi /home/fragua/anaconda/lib/5.26.2 .) at /home/fragua/RM/RepeatMasker/Taxonomy.pm line 80.
BEGIN failed--compilation aborted at /home/fragua/RM/RepeatMasker/Taxonomy.pm line 80.
Compilation failed in require at ./RepeatMasker line 310.
BEGIN failed--compilation aborted at ./RepeatMasker line 310.
I installed RepeatMasker in another computer without problems, but I don't know why now I encontered this problem
You have two builds of Perl installed:
/usr/bin/perl
/home/fragua/anaconda/bin/perl.
/home/fragua/anaconda/bin/perl is first in your PATH. This means that programs with the following shebang (#!) line will use /home/fragua/anaconda/bin/perl:
#!/usr/bin/env perl
RepeatMasker appears to be such a program.
All of this is fine.
The Problem
/home/fragua/anaconda/bin contains the scripts installed by /home/fragua/anaconda/bin/perl. As part of the installation process of these scripts, the shebang line of these scripts should have been rewritten to specify /home/fragua/anaconda/bin/perl.
However, the shebang line of /home/fragua/anaconda/bin/cpan references /usr/bin/perl. This means that using /home/fragua/anaconda/bin/cpan would install modules for /usr/bin/perl, not /home/fragua/anaconda/bin/perl.
The Workaround
You could avoid relying on the shebang line and explicitly specify the correct perl.
/home/fragua/anaconda/bin/perl /home/fragua/anaconda/bin/cpan Text::Soundex
Or, given your $PATH,
perl /home/fragua/anaconda/bin/cpan Text::Soundex
The Fix
To fix this problem in an ongoing manner requires changing the shebang lines of the scripts to be what they should be. In every file in /home/fragua/anaconda/bin (and in particular for cpan), replace
#!/usr/bin/perl
with
#!/home/fragua/anaconda/bin/perl
You could do this use the following (which does a backup of the files it changes):
perl -0777ne'print "$ARGV\n" if m{^#!\s*/usr/bin/perl\b}' /home/fragua/anaconda/bin/* \
| xargs perl -i~ -0777pe's{^#!\s*/usr/bin/perl\b}{#!/home/fragua/anaconda/bin/perl}'
I'm trying to run a perl script that is located in a remote linux server from windows using the python program. I'm using the subprocess.call method.
This is the python line of code
returnCd = subprocess.call(['plink', '-ssh', \
'%s#%s' %('******','*****.***.com'), '-pw', '****', \
'perl', '/apps/CACSGDEV/springbatch/perlscript/DEBTOR_VERIFICATION.pl'], \
shell=True)
And this is what i see in the console (broken over lines for readability)
Can't locate ENVRC.pl in #INC (#INC contains: /usr/local/lib64/perl5
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .)
at /apps/CACSGDEV/springbatch/perlscript/DEBTOR_VERIFICATION.pl line 16.
The file DEBTOR_VERIFICATION.pl has the following # line 16
require "ENVRC.pl";
The file ENVRC.pl is in the same path as that of the DEBTOR_VERIFICATION.pl. Can anyone please suggest?
The program DEBTOR_VERIFICATION.pl is directly executed and thus it doesn't need to have its directory in #INC. On the other hand, when a file need be loaded via require (or use, which uses require) then it is precisely the directories in #INC that are searched for it. Since /apps/.., where ENVRC.pl resides, is not there the file cannot be found.
You need to add that directory to #INC and a good way to do it is via lib pragma
use warnings;
use strict;
...
use lib "/apps/CACSGDEV/springbatch/perlscript";
...
But if this program (DEBTOR_VERIFICATION.pl) and the required file ENVRC.pl will always stay in the same directory it is better to use FindBin instead of hard coding the path
use warnings;
use strict;
...
use FindBin qw($RealBin);
use lib $RealBin;
In either case the files in that directory can now be found by use and require (and do).
The DEBTOR program works when executed right from its directory, in older Perls, since the . (the current working directory) used to be included in #INC by default. We see that this is the case from #INC printed in the error message. So . gets searched and ENVRC.pl is found.
Relying on that has really always been a bad practice, but as of perl v5.26.0 (perldelta) (May 2017) the . directory is not in #INC anymore.
So you should add the above use lib statement to the DEBTOR... program anyway.
I am trying to run script which uses XML/LibXML package.
But, XML/LibXML package is already installed. I ran following command:
perl -MXML::LibXML -e 1. it did not give any output, that means this package is installed.
when i ran my script. Following error occured.
Can't locate XML/LibXML.pm in #INC (#INC contains:
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
.). BEGIN failed--compilation aborted.
One more point to note is there is no directory "5.8.8" under /usr/lib64/perl5/site_perl/
Please suggest to overcome this issue.
There are three possibilities:
You have two installs of perl and you script is using the "wrong" one.
Either install XML::LibXML using the perl used by the script, or replace the script's shebang (#!) line with the output of the following:
perl -MXML::LibXML -le'print "#!".$^X'
Differences in the environment.
If XML::LibXML was installed in a nonstandard directory, it could be that PERL5LIB was used to communicate this to perl when you executed your test, but not when you run the script.
A permission issue.
This isn't very likely.
If the script is run as the same user as your test, it's not a permission issue.
If it is a permission issue, make sure the library directory is accessible to the user executing the script.
I see this a lot in bash scripts and I cannot see this in the manual and other sites.
What does the -I in running a perl script mean?
It is run like this:
perl -I$prod_dir $prod_dir/script.pl <parameter1> <parameter2>
Can someone explain it to me?
-Idirectory
Directories specified by -I are prepended to the search path for modules (#INC ).
Source: perlrun documentation
It means perl will include the modules available under specified directory following -I which is $prod_dir in your case.
By default Perl picks up modules from #INC. If you want to use a module which is not available in #INC then you can specify the directory using -I. This specified directory will be appended to #INC at run time.
Also read:
How is Perl's #INC constructed? (aka What are all the ways of affecting where Perl modules are searched for?)
How to change #INC to find Perl modules in non-standard locations
I am trying my hands for the first time in -> Apache - Perl (CGI) on Ubuntu.
The Apache server is working fine in the folder /var/www for the default index.html file. But since I want to run a CGI script, I also installed (just in case) DBI, as suggested by some forums. I set the permissions for complete access to my cgi-bin folder in which the select.cgi script resides. I tried tweaking the select.cgi script multiple times redirecting the library to the Perl library, but to no avail. I modified the httpd.conf file and set the directory path to the select.cgi folder. That didn't work. I also defined ScriptAlias, and set it to the working directory. That didn't work either.
Does anyone have any helpful pointers. Thanks.
This is not exact solution that you want but the overall idea is like below.
How to resolve Cant locate xxxx.pm in #INC path problem
By default perl looks for modules in the standard library path and the current directory.
Sometimes you need to use some modules that are installed in non standard locations; there are several ways to deal with this situation:
To check whether your module is in #INC path use.
Example:
perl -e 'use SOAP::Lite;'
perl -e 'use Error;'
If you run these commands on a system that has SOAP::Lite and Error installed, Perl will simply return from these commands without printing any output.
To check current standard library path use:
perl -le 'print foreach #INC'
If you have the administrative privileges, then best solution is to install the module in any of the system defined library path.
Set the environment variable PERL5LIB
Perl will look for modules in the directories specified in PERL5LIB environment variable before looking in the standard library and current directory.
So you can set this variable to locate your modules.
Example:
# For unix like systems
PERL5LIB=/home/path/lib:/usr/another/path/lib; export PERL5LIB
Note: separate the directories with colons on unix and with a semicolon on Windows.
IF you are running your code from command line then use -I parameter. The syntax should be something like.
perl -I /home/path/lib -I /usr/another/lib script.pl
And you can also Add the library path in your script
The command for including the path in your script is: use lib path.
Example:
#!/usr/bin/perl
use lib "/home/path/lib";
use lib "/usr/another/lib";
use MyCustomModule;
In a comment, you gave information that contradicts what you gave originally. The latter information appears to be more reliable, so I'll use it.
I believe you said the path to the module is
/usr/lib/perl5/vendor_perl/5.8.5/foo/bar/Connection.pm
and that the error message you got (with line breaks added) is:
Can't locate foo/bar/Connection.pm in #INC (#INC contains:
/etc/perl
/usr/local/lib/perl/5.14.2
/usr/local/share/perl/5.14.2
/usr/lib/perl5
/usr/share/perl5
/usr/lib/perl/5.14
/usr/share/perl/5.14
/usr/local/lib/site_perl
.
/usr/lib/perl5/vendor_perl/5.8.5/foo/bar/
) at ...
You did something like
use foo::bar::Connection;
or
require "foo/bar/Connection.pm";
Perl looked for
/etc/perl/foo/bar/Connection.pm
/usr/local/lib/perl/5.14.2/foo/bar/Connection.pm
...
/usr/lib/perl5/vendor_perl/5.8.5/foo/bar/foo/bar/Connection.pm
But none of those are
/usr/lib/perl5/vendor_perl/5.8.5/foo/bar/Connection.pm
It's simple to fix. Add the following to your script:
use lib '/usr/lib/perl5/vendor_perl/5.8.5';
The other possible fix is to use
use Connection;
instead of
use foo::bar::Connection;
Which fix is the correct fix depends on what that package line in side the module looks like. If you find package foo::bar::Connection;, you need to modify #INC (as shown with use lib, for example). If you findpackage Connection;, you need to change theuse` directive.