Install BioPerl Package with "cpanm"
Q
How to install BioPerl package with "cpanm" command?
✍: FYIcenter.com
A
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 CPAN.pm 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: http://www.cpan.org/authors/01mailrc.txt.gz Reading '/root/.local/share/.cpan/sources/authors/01mailrc.txt.gz' CPAN: Compress::Zlib loaded ok (v2.081) ............................................................................DONE Fetching with HTTP::Tiny: http://www.cpan.org/modules/02packages.details.txt.gz Reading '/root/.local/share/.cpan/sources/modules/02packages.details.txt.gz' Database was generated on Sat, 30 May 2020 04:55:53 GMT ...............................................................DONE Fetching with HTTP::Tiny: http://www.cpan.org/modules/03modlist.data.gz Reading '/root/.local/share/.cpan/sources/modules/03modlist.data.gz' DONE Writing /root/.local/share/.cpan/Metadata Running install for module 'App::cpanminus' Fetching with HTTP::Tiny: http://www.cpan.org/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz CPAN: Digest::SHA loaded ok (v6.02) Fetching with HTTP::Tiny: http://www.cpan.org/authors/id/M/MI/MIYAGAWA/CHECKSUMS 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 MIYAGAWA/App-cpanminus-1.7044.tar.gz /usr/bin/perl Makefile.PL -- OK Running make for M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz cp lib/App/cpanminus.pm blib/lib/App/cpanminus.pm cp lib/App/cpanminus/fatscript.pm blib/lib/App/cpanminus/fatscript.pm 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 MIYAGAWA/App-cpanminus-1.7044.tar.gz /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 MIYAGAWA/App-cpanminus-1.7044.tar.gz /bin/make test -- OK Running make install Manifying 1 pod document Manifying 2 pod documents Installing /usr/local/share/perl5/App/cpanminus.pm Installing /usr/local/share/perl5/App/cpanminus/fatscript.pm 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 MIYAGAWA/App-cpanminus-1.7044.tar.gz /bin/make install -- OK
2. Run "cpanm" command to install BioPerl:
fyicenter$ sudo /usr/local/bin/cpanm BioPerl --> Working on BioPerl Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.7.tar.gz ... 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 http://www.cpan.org/authors/id/J/JH/JHI/Graph-0.9704.tar.gz ... OK Configuring Graph-0.9704 ... OK Building and testing Graph-0.9704 ... OK Successfully installed Graph-0.9704 --> Working on XML::DOM Fetching http://www.cpan.org/authors/id/T/TJ/TJMATHER/XML-DOM-1.46.tar.gz ... OK Configuring XML-DOM-1.46 ... OK ==> Found dependencies: XML::Parser::PerlSAX, LWP::UserAgent, XML::Parser, XML::RegExp --> Working on XML::Parser::PerlSAX Fetching http://www.cpan.org/authors/id/K/KM/KMACLEOD/libxml-perl-0.08.tar.gz ... OK Configuring libxml-perl-0.08 ... OK ==> Found dependencies: XML::Parser --> Working on XML::Parser Fetching http://www.cpan.org/authors/id/T/TO/TODDR/XML-Parser-2.46.tar.gz ... OK Configuring XML-Parser-2.46 ... OK ==> Found dependencies: LWP::UserAgent --> Working on LWP::UserAgent Fetching http://www.cpan.org/authors/id/O/OA/OALDERS/libwww-perl-6.44.tar.gz ... 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, HTTP::Cookies ... ==> 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 http://www.cpan.org/authors/id/M/MI/MIROD/XML-DOM-XPath-0.14.tar.gz ... 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 http://www.cpan.org/authors/id/M/MI/MIROD/XML-DOM-XPath-0.14.tar.gz ... 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 http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.7.tar.gz ... 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.org
2023-02-28, 516🔥, 0💬
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