Install BioPerl Package with "cpanm"


How to install BioPerl package with "cpanm" command?



Using "cpanm" command is the best option to install the BioPerl distribution package automatically as shown in this tutorial on a CentOS computer:

1. Make sure that you have "cpanm" command installed. If not run the command below:

fyicenter$ sudo cpan App::cpanminus

Loading internal null logger. Install Log::Log4perl for logging messages requires configuration, but most of it can be done automatically.
If you answer 'no' below, you will enter an interactive dialog for each
configuration option instead.

Would you like to configure as much as possible automatically? [yes] yes
CPAN: HTTP::Tiny loaded ok (v0.074)
Fetching with HTTP::Tiny:
Reading '/root/.local/share/.cpan/sources/authors/01mailrc.txt.gz'
CPAN: Compress::Zlib loaded ok (v2.081)
Fetching with HTTP::Tiny:
Reading '/root/.local/share/.cpan/sources/modules/02packages.details.txt.gz'
  Database was generated on Sat, 30 May 2020 04:55:53 GMT
Fetching with HTTP::Tiny:
Reading '/root/.local/share/.cpan/sources/modules/'
Writing /root/.local/share/.cpan/Metadata
Running install for module 'App::cpanminus'
Fetching with HTTP::Tiny:
CPAN: Digest::SHA loaded ok (v6.02)
Fetching with HTTP::Tiny:
Checksum for /root/.local/share/.cpan/sources/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz ok
'YAML' not installed, will not store persistent state
CPAN: CPAN::Meta::Requirements loaded ok (v2.140)
CPAN: Parse::CPAN::Meta loaded ok (v2.150010)
CPAN: CPAN::Meta loaded ok (v2.150010)
CPAN: Module::CoreList loaded ok (v5.20181130)
Configuring M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for App::cpanminus
Writing MYMETA.yml and MYMETA.json
  /usr/bin/perl Makefile.PL -- OK
Running make for M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz
cp lib/App/ blib/lib/App/
cp lib/App/cpanminus/ blib/lib/App/cpanminus/
cp bin/cpanm blib/script/cpanm
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/cpanm
Manifying 1 pod document
Manifying 2 pod documents
  /bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" ...
t/happy_cpantesters.t .. 1/1 # App::cpanminus/1.7044
t/happy_cpantesters.t .. ok   
All tests successful.
Files=1, Tests=1,  0 wallclock secs ( 0.01 usr  0.00 sys +  0.03 cusr  0.00 csys =  0.04 CPU)
Result: PASS
  /bin/make test -- OK
Running make install
Manifying 1 pod document
Manifying 2 pod documents
Installing /usr/local/share/perl5/App/
Installing /usr/local/share/perl5/App/cpanminus/
Installing /usr/local/share/man/man1/cpanm.1
Installing /usr/local/share/man/man3/App::cpanminus.3pm
Installing /usr/local/share/man/man3/App::cpanminus::fatscript.3pm
Installing /usr/local/bin/cpanm
Appending installation info to /usr/lib64/perl5/perllocal.pod
  /bin/make install  -- OK

2. Run "cpanm" command to install BioPerl:

fyicenter$ sudo /usr/local/bin/cpanm BioPerl
--> Working on BioPerl
Fetching ... OK
Configuring BioPerl-1.7.7 ... OK
==> Found dependencies: Graph::Directed, XML::DOM, XML::SAX, XML::LibXML::Reader, 
   HTTP::Request::Common, Test::Weaken, XML::Writer, IPC::Run, LWP::UserAgent, 
   XML::DOM::XPath, IO::String, Test::Most, List::MoreUtils, Data::Stag, XML::LibXML, 
   XML::SAX::Base, XML::SAX::Writer, Test::Memory::Cycle, Set::Scalar, 
   XML::Parser::PerlSAX, IO::Scalar, Test::RequiresInternet, Error, HTTP::Response, 
   XML::Twig, YAML
--> Working on Graph::Directed
Fetching ... OK
Configuring Graph-0.9704 ... OK
Building and testing Graph-0.9704 ... OK
Successfully installed Graph-0.9704
--> Working on XML::DOM
Fetching ... OK
Configuring XML-DOM-1.46 ... OK
==> Found dependencies: XML::Parser::PerlSAX, LWP::UserAgent, XML::Parser, XML::RegExp

--> Working on XML::Parser::PerlSAX
Fetching ... OK
Configuring libxml-perl-0.08 ... OK
==> Found dependencies: XML::Parser

--> Working on XML::Parser
Fetching ... OK
Configuring XML-Parser-2.46 ... OK
==> Found dependencies: LWP::UserAgent

--> Working on LWP::UserAgent
Fetching ... OK
Configuring libwww-perl-6.44 ... OK
==> Found dependencies: LWP::MediaTypes, File::Listing, Test::Needs, 
   HTML::Entities, Net::HTTP, HTTP::Date, HTTP::Status, HTTP::Request::Common, 
   WWW::RobotRules, HTTP::Negotiate, HTML::HeadParser, HTTP::Response, 
   HTTP::Request, Try::Tiny, HTTP::Daemon, Test::Fatal, Test::RequiresInternet, 
==> Found dependencies: Test::Fatal
==> Found dependencies: HTTP::Date
==> Found dependencies: Time::Zone
==> Found dependencies: HTML::Tagset
==> Found dependencies: Clone, IO::HTML, Encode
==> Found dependencies: Module::Build::Tiny
==> Found dependencies: ExtUtils::Helpers, ExtUtils::InstallPaths, ExtUtils::Config
==> Found dependencies: ExtUtils::Config
==> Found dependencies: XML::SAX::Base, XML::NamespaceSupport
==> Found dependencies: Alien::Base::Wrapper, Alien::Libxml2
==> Found dependencies: File::chdir, Path::Tiny, FFI::CheckLib, Capture::Tiny, Test2::V0
==> Found dependencies: Test2::V0, Test2::Require::Module, Test2::Require::EnvVar
==> Found dependencies: Importer
==> Found dependencies: Sort::Versions
==> Found dependencies: XML::XPathEngine
==> Found dependencies: Test::Warn, Test::Differences, Test::Deep, Test::Exception, Exception::Class
==> Found dependencies: Sub::Uplevel
==> Found dependencies: Devel::StackTrace, Class::Data::Inheritable
==> Found dependencies: List::MoreUtils::XS, Exporter::Tiny, Test::LeakTrace
==> Found dependencies: XML::Filter::BufferText
==> Found dependencies: PadWalker, Devel::Cycle
==> Found dependencies: Test::YAML
==> Found dependencies: Test::Base
==> Found dependencies: Spiffy
! Installing the dependencies failed: Module 'XML::DOM::XPath' is not installed
! Bailing out the installation for BioPerl-1.7.7.
80 distributions installed

3. Try to install 'XML::DOM::XPath' with "cpanm" command.

fyicenter$ sudo /usr/local/bin/cpanm XML::DOM::XPath
--> Working on XML::DOM::XPath
Fetching ... OK
Configuring XML-DOM-XPath-0.14 ... OK
Building and testing XML-DOM-XPath-0.14 ... FAIL
! Installing XML::DOM::XPath failed. See /root/.cpanm/work/1590823188.5848/build.log 
for details. Retry with --force to force install it.

4. Read the error message in the log file:

fyicenter$ sudo tail /root/.cpanm/work/1590823188.5848/build.log 
Test Summary Report
t/test_non_ascii.t                  (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 10 tests but ran 0.
Files=35, Tests=183,  2 wallclock secs ( 0.07 usr  0.02 sys +  1.95 cusr  0.20 csys =  2.24 CPU)
Result: FAIL
Failed 1/35 test programs. 0/183 subtests failed.
make: *** [Makefile:842: test_dynamic] Error 255
-> FAIL Installing XML::DOM::XPath failed. See 
   /root/.cpanm/work/1590823188.5848/build.log for details. Retry with --force to force install it.

5. Try it again with the "--force" option to by-pass the testing error.

fyicenter$ sudo /usr/local/bin/cpanm XML::DOM::XPath --force 
--> Working on XML::DOM::XPath
Fetching ... OK
Configuring XML-DOM-XPath-0.14 ... OK
Building and testing XML-DOM-XPath-0.14 ... FAIL
! Testing XML-DOM-XPath-0.14 failed but installing it anyway.
Successfully installed XML-DOM-XPath-0.14
1 distribution installed

6. Re-install "BioPerl".

fyicenter$ sudo /usr/local/bin/cpanm BioPerl
--> Working on BioPerl
Fetching ... 
Configuring BioPerl-1.7.7 ... OK
Building and testing BioPerl-1.7.7 ... OK
Successfully installed BioPerl-1.7.7
1 distribution installed


Install BioPerl Package Manually

HOWTO Documents at

BioPerl - Perl Bioinformatics Toolkit

⇑⇑ OBF (Open Bioinformatics Foundation) Tools

2023-02-28, 262🔥, 0💬