I tried to upgrade my custom perl version from 5.10.1 to 5.16.3, and now I am getting following errors in my logs:
[Wed May 21 00:05:32 2014] [error] Can't locate unicore/Canonical.pl
in #INC (#INC contains: /opt/test/perl/lib/5.10.1/i686-linux
/opt/test/perl/lib/5.10.1
/opt/test/perl/lib/site_perl/5.10.1/i686-linux
/opt/test/perl/lib/site_perl/5.10.1 . /opt/test/httpd) at
/opt/test/perl/lib/5.10.1/utf8_heavy.pl line 139.\n
Can anyone please help me to sort it out?
try re-installing the missing modules using cpan.
the "upgrade" probably created a second, parallel Perl installation on your system...
did you then remove the 'old' version?
Follow below commands:
1/ Install cpan with yum install cpan or apt-get install cpan
2/ On the command prompt enter: cpan install unicore:Canonical
Related
I am trying to install a software called prokka(http://www.vicbioinformatics.com/software.prokka.shtml)
But i got a error in installation.
I tried install as indicated via git hub clone:
and got this:
Can't locate XML/Simple.pm in #INC (you may need to install the XML::Simple module) (#INC contains: /home/paulo/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/paulo/anaconda3/lib/site_perl/5.26.2 /home/paulo/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /home/paulo/anaconda3/lib/5.26.2 .) at /home/paulo/prokka/bin/prokka line 29.
BEGIN failed--compilation aborted at /home/paulo/prokka/bin/prokka line 29.
I tried to install the XML with:
sudo cpan install
But not worked to.
I also installed successively all other dependencies as asked but seems not work.
Then I tried with conda and got this:
ERROR conda.core.link:_execute(700): An error occurred while
installing package 'bioconda::perl-algorithm-diff-1.1903-pl526_2'.
Rolling back transaction: done [Errno 13] Permission denied:
'/home/paulo/anaconda3/lib/site_perl/5.26.2/Algorithm' ()
Now I dont know what else to do.
Any help?
Thank you by your time.
Paulo
I tried to install the XML with: sudo cpan install But not worked to.
It would be helpful to know exactly how this failed. What error messages you got.
You don't say what kind of system you're trying to work on, but if you're using a Linux distribution, it's almost certain that there's a pre-build package for XML::Simple. Try sudo dnf install Perl-XML-Simple on a Red Hat-based system and sudo apt-get install libxml-simple-perl on a Debian-based system.
Just make a conda update all, crate a env prokka and it was done.
Thank you for your help and time guys.
Paulo
So I am trying to run a perl script on my Centos machine. I have tried on Centos 5,6,7 with no success. Every time I run the script I get this:
Can't locate Net/SSH2.pm 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 .)
I have installed libssh2
Package libssh2-1.4.3-12.el7.x86_64 already installed and latest version
I have tried using cpan but no matter what I do it doesn't seem to work.
I just don't understand why perl isn't finding the module... Am I missing something?
If somebody could guide me to actually installing the SSH2 module because I have looked everywhere and nothing seems to work.
Thanks in advance.
UPDATE:
When I try to install via cpan:
cpan[1]> install Net::SSH2
Reading '/root/.cpan/Metadata'
Reading '/root/.cpan/sources/authors/01mailrc.txt.gz'
........................................................................DONE
Reading '/root/.cpan/sources/modules/02packages.details.txt.gz'
Database was generated on Fri, 04 Jan 2019 22:17:03 GMT
HTTP::Date not available
.............
New CPAN.pm version (v2.22) available.
[Currently running version is v1.9800]
You might want to try
install CPAN
reload cpan
to both upgrade CPAN.pm and run the new version without leaving
the current session.
........................................Killed
Still getting the same error...
libssh is the C library for SSH. Net::SSH2 is a Perl module. They are different piece of software (although Net::SSH2 probably depends on libssh).
You need to install Net::SSH2.
See What's the easiest way to install a missing Perl module?
As Quentin mentioned in his answer, libssh2 is the C library for SSH, whereas Net::SSH2 is a Perl module. Since Net::SSH2 will be installed from source (which is what the cpan command does in the background), you will need to ensure that a few prerequisites are installed:
sudo yum install libssh2 libssh2-devel gcc
The libssh2 package was added to this list for completeness. The development package for libssh2 (libssh2-devel) as well as gcc (a C compiler) are required, since the process of installing Net::SSH2 from source requires a library to be built so that Net::SSH2 can talk to libssh2.
When Perl modules are installed from source, the module's test suite is run by default to check that everything is ok before actually running the install step. Hence, you will need to ensure that perl-Test-Simple is installed, since Net::SSH2 uses this to run its tests:
sudo yum install perl-Test-Simple
I personally find it much easier to install Perl modules via cpanm than cpan, thus I recommend installing it (it's available as a yum package):
sudo yum install perl-App-cpanminus
Now the installation of Net::SSH2 should be as simple as:
cpanm Net::SSH2
If you want to install the module system-wide, then you will need to prefix the cpanm call with sudo:
sudo cpanm Net::SSH2
I am installing perl module "WWW::Curl::Easy" but it's getting error I also use by fource install but it's getting same error. why this is happend plz help me out.
I used these command in cpan
perl -MCPAN -e shell
force install WWW::Curl::Easy
cpan[1]> force install WWW::Curl::Easy
Reading '/root/.cpan/Metadata'
Database was generated on Thu, 16 Feb 2017 05:17:02 GMT
Running install for module 'WWW::Curl::Easy'
Checksum for /root/.cpan/sources/authors/id/S/SZ/SZBALINT/WWW-Curl-4.17.tar.gz ok
Scanning cache /root/.cpan/build for sizes
............................................................................DONE
Configuring S/SZ/SZBALINT/WWW-Curl-4.17.tar.gz with Makefile.PL
Locating required external dependency bin:curl-config... missing.
Unresolvable missing external dependency.
Please install 'curl-config' seperately and try again.
NA: Unable to build distribution on this platform.
No 'Makefile' created SZBALINT/WWW-Curl-4.17.tar.gz
/usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK
Failed during this command:
SZBALINT/WWW-Curl-4.17.tar.gz : writemakefile NO -- No 'Makefile' created
I use this and it's install "WWW::Curl::Easy" Module without any error
apt-get install libwww-curl-perl
On Red Hat try:
yum install curl curl-devel
installing only curl didn't work for me.
It is telling you the problem
Locating required external dependency bin:curl-config... missing.
Unresolvable missing external dependency. Please install 'curl-config'
seperately and try again.
So install curl-config and try again. Always check for dependencies.
Installing curl-config methods depends on the OS.
for Redhat for instance it will be
yum install curl
FreeBSD 12.2-RELEASE
cd /usr/ports/www/p5-WWW-Curl
make install clean
...
(cleaning for curl-7.80.0
cleaning for p5-WWW-Curl)
I need to install Padre on ActivePerl 5.16.2. But there are no Padre ppm packages and
cpan Padre says:
MDOOTSON/Alien-wxWidgets-0.64.tar.gz
C:\Perl\site\bin\dmake.exe -- NOT OK
CPAN: YAML::XS loaded ok (v0.38)
Running make test
Can't test without successful make
Running make install
Make had returned bad status, install seems impossible
Running make for P/PL/PLAVEN/Padre-0.98.tar.gz
Warning: Prerequisite 'Alien::wxWidgets => 0.62' for 'PLAVEN/Padre-0.98.tar.gz' failed when processing 'MDOOTSON/Alien-wxWidgets-0.64.tar
CPAN: Time::HiRes loaded ok (v1.9725)
CPAN.pm: Building P/PL/PLAVEN/Padre-0.98.tar.gz
Set up gcc environment - 3.4.5 (mingw-vista special r3)
Can't locate Alien/wxWidgets.pm in #INC (#INC contains: inc privinc C:\Perl\dbg C:/Perl/site/lib C:/Perl/lib .) at Makefile.PL line 52.
BEGIN failed--compilation aborted at Makefile.PL line 52.
Warning: No success on command[C:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site]
PLAVEN/Padre-0.98.tar.gz
C:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site -- NOT OK
Running make test
Make had some problems, won't test
Running make install
Make had some problems, won't install
Could not read metadata file. Falling back to other methods to determine prerequisites
tl;dr Padre for ActivePerl 5.16 has not been released yet.
The following contents are just me trying to make it work.
First I tried:
cpan Padre
I did this three times, but "dmake.exe" always failed.
There was no reference about this error on the Internet.
Secondly I tried PPM with an article in Padre Wiki:
ppm rep add wxperl http://www.wxperl.co.uk/repository
ppm install Alien-wxWidgets
ppm install Wx
ppm install Padre
but the very last line claimed:
ppm install failed: Can't find any package that provides Padre
Finally I couldn't help talking to the Padre developers:
So, apparently we have nothing to do but wait for them to develop it.
Or you can participate to the development, of course!
This post should help: Installation instructions for Wx (wxWidgets fomerly wxWindows) using ActivePerl
I need to use WebKit in my perl + gtk2 application. Found a package Gtk2::WebKit on CPAN, but can't get it working.
cpan> install Gtk2::WebKit
gives following output:
Package webkit-1.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `webkit-1.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'webkit-1.0' found
at inc/Module/Install/PRIVATE/WebKit.pm line 24
*** can not find package webkit-1.0
*** check that it is properly installed and available in PKG_CONFIG_PATH
at inc/Module/Install/PRIVATE/WebKit.pm line 24
No 'Makefile' created'YAML' not installed, will not store persistent state
FLORA/Gtk2-WebKit-0.09.tar.gz
/usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK
Running make test
Make had some problems, won't test
Running make install
Make had some problems, won't install
Failed during this command:
FLORA/Gtk2-WebKit-0.09.tar.gz : writemakefile NO -- No 'Makefile' created
It looks as if cpan wasn't able to find webkit, but I'm not sure how to fix that (my first time using perl and cpan).
Env: perl 5.12.4, ubuntu 11.10
Install libwebkitgtk-devel: sudo apt-get install libwebkitgtk-devel.
sudo apt-get install libwebkitgtk-dev
For Debian/Ubuntu and similar, the package name to install is libwebkitgtk-dev.
For OpenSuse and other RPM-based systems, the package name is libwebkitgtk-devel.