I trying to run a Perl script (taxid2wgs.pl) used in searching a taxonomic subset of WGS.
taxid2wgs.pl (available at ftp://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS).
$ ./taxid2wgs.pl -title "Bacteria WGS" -alias_file bacteria-wgs 2
Here, 2 is the taxid for Bacteria. taxid2wgs.pl will produce the alias file "bacteria-wgs.nvl".
However I got an error message below.
Can't locate LWP/UserAgent.pm in #INC (you may need to install the LWP::UserAgent module) (#INC contains: /usr/local/lib/perl5/site_perl/5.24.0/x86_64-linux-thread-multi /usr/local/lib/perl5/site_perl/5.24.0 /usr/local/lib/perl5/5.24.0/x86_64-linux-thread-multi /usr/local/lib/perl5/5.24.0 .) at ./taxid2wgs.pl line 4.
BEGIN failed--compilation aborted at ./taxid2wgs.pl line 4.
What I do next is install the LWP perl module (libwww-perl-6.05).
~# perl Makefile.PL
Checking if your kit is complete...
perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/List/Util/Util.so: undefined symbol: Perl_xs_handshake
Before posting, I've tried to another solution.
~# perl -MCPAN -e 'install Bundle::LWP'
perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/List/Util/Util.so: undefined symbol: Perl_xs_handshake
To overcome the problem, I used YUM to install the required module named perl-libwww-perl.
~# yum install perl-libwww-perl
But it still doesn't work for my operation.
Sorry, I'm very new to this. Appreciate the help!
I had the same issue. And like others have said, this is because the program uses a different perl. I got the error when I used perl 5.24.0, but the program worked with perl-5.18.2.
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 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 "#!".$^X'
Differences in the environment.
If XML::LibXML was installed in a nonstandard directory, it could be that PERL5LIB was used to communicate this to perl when you executed your test, but not when you run the script.
A permission issue.
This isn't very likely.
If the script is run as the same user as your test, it's not a permission issue.
If it is a permission issue, make sure the library directory is accessible to the user executing the script.
I have created one perl xsub to call a C function from my perl script.But the problem is that I cannot install that xsub directly by "make install'.The xsub has been created by make command already in the mentioned folder.I have to use it without installing it.Also I am using Perl packager to create executable for my perl script.here is my make file-
PP=/usr/local/bin/pp
INSTALL=/usr/bin/install
PROG=nsgslbautosync
SDIR=../scripts
SRCS=$(SDIR)/syncgslbconfig.pl
nsgslbautosync:$(SRCS)
$(PP) --lib GslbSync/lib/GslbSync.pm --link GslbSync/blib/arch/auto/GslbSync/GslbSync.so -o $# $<
Now the problem is that even after linking the xsub,I am getting the following error on running the script-
Can't locate GslbSync.pm in #INC (#INC contains: CODE(0x802941930)/var/tmp/par-726f6f74/cache-dbeb96ca0c7f9489e2bfc7a2fc11650939727dbd/inc/lib /var/tmp/par-726f6f74/cache-dbeb96ca0c7f9489e2bfc7a2fc11650939727dbd/inc CODE(0x80226dde0)CODE(0x802276060)) at script/syncgslbconfig.pl line 20.
BEGIN failed--compilation aborted at script/syncgslbconfig.pl line .ERROR:
I even tried to link the xsub in my script by using "use lib" but no luck, got the same error.
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.
Gettin below error while running my perl file
Can't locate HTML/TreeBuilder/XPath.pm in #INC (#INC contains: C:/Perl/lib C:/Pe
rl/site/lib .) at display.pl line 4.
BEGIN failed--compilation aborted at display.pl line 4.
HTML::TreeBuilder::XPath module(0.14) is installed. From command line when i run command
perl -e HTML::TreeBuilder::XPath it doesn't give any error.
when i run from command line perldoc -l HTML::TreeBuilder::XPath gives below error:
No documentation found for "HTML::TreeBuilder::XPath".
My perl version is 5.8.7
First cross check does this module is really installed ? I think it is not installed, install it from cpan.