[Bioperl-l] installing bioperl on an SGI w/freeware perl, gcc, etc.

[Jason Stajich]

Did you try and upgrade your ExtUtils::MakeMaker to the latest version?
  http://bugzilla.bioperl.org/show_bug.cgi?id=1351

An "arg list too long Bioperl" Google search also pulls up the old list
messages about this as well.  I think we probably need to incorporate a
coherent summary of this info into the PLATFORMS and INSTALL doc.

-jason
On Tue, 22 Jul 2003, Wes Barris wrote:

> Can anyone enlighten me on how to install bioperl on an SGI running
> IRIX 6.5.18?  I do not have the SGI "cc" compiler.  Instead I have
> the freeware versions of gcc-3.2.1, gmake-3.80, perl-5.6.1, etc.
>
> I have modified my /usr/freeware/lib/perl5/5.6.1/irix-n32/Config.pm
> file as described here:
>
> http://www.digitalmages.com/irix/#perl
>
> Then, in bioperl-1.2.2, I do this:
>
> perl Makefile.PL
>
> Then I do this:
>
> wes at structure> gmake
> gmake: execvp: /bin/sh: Arg list too long
> gmake: *** [pm_to_blib] Error 127
>
>
> If I try using regular make I get this:
>
> wes at structure> make
> *** Termination code 138 (bu21)
>
>
> Here is the full output of running perl Makefile.PL:
>
> wes at structure> perl Makefile.PL
> Generated sub tests. go make show_tests to see available subtests
>
> External Module LWP::UserAgent, Part of the LWP package,
>   is not installed on this computer.
>    The Bio::DB::*,Bio::Tools::Run::RemoteBlast in Bioperl needs it for GenBank+GenPept
> sequence retrieval, remote http Blast jobs
>
> External Module HTTP::Request::Common, Part of the LWP package,
>   is not installed on this computer.
>    The Bio::DB::*,Bio::Tools::Run::RemoteBlast in Bioperl needs it for GenBank+GenPept
> sequence retrieval, remote http Blast jobs
>
> External Module SOAP::Lite, SOAP protocol,
>   is not installed on this computer.
>    The Bio::DB::XEMBLService in Bioperl needs it for XEMBL Services (also Bibliographic
> queries in Biblio::)
>
> External Module Text::Shellwords, Execute shell commands,
>   is not installed on this computer.
>    The Bio::Graphics in Bioperl needs it for test scripts
>
> External Module HTML::Parser, HTML parsing,
>   is not installed on this computer.
>    The Bio::DB::GDB in Bioperl needs it for HTML parsing of GDB page
>
> External Module DBD::mysql, Mysql driver,
>   is not installed on this computer.
>    The Bio::DB::GFF in Bioperl needs it for loading and querying of Mysql-based GFF
> feature databases
>
> External Module Ace, Aceperl,
>   is not installed on this computer.
>    The Bio::DB::Ace in Bioperl needs it for access of ACeDB database
>
> External Module GD, Graphical Drawing Toolkit,
>   is not installed on this computer.
>    The Bio::Graphics in Bioperl needs it for Rendering Sequences and Features
>
> External Module XML::Twig, Available on CPAN,
>   is not installed on this computer.
>    The Module Bio::Variation::IO::xml.pm in Bioperl needs it for parsing of XML documents
>
> External Module Storable, Persistent object storage and retrieval,
>   is not installed on this computer.
>    The Bio::DB::FileCache in Bioperl needs it for Storing sequence objects in local file cache
>
> External Module XML::Parser::PerlSAX, Parsing of XML documents,
>   is not installed on this computer.
>    The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation code,
> GAME parser
>
> External Module XML::Parser, Parsing of XML documents,
>   is not installed on this computer.
>    The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation code,
> GAME parser
>
> External Module Graph::Directed, Generic Graph data stucture and algorithms,
>   is not installed on this computer.
>    The Bio::Ontology::SimpleOntologyEngine in Bioperl needs it for Ontology Engine
> implementation for the GO parser
>
>
> Information:
>
>     There are some external packages and perl modules, listed above, which
>     bioperl uses. This only effects the functionality which is listed above:
>     the rest of bioperl will work fine, which includes nearly all of the
>     core packages.
>
>     The installation of these external packages is very simple. You
>     can read more about bioperl external dependencies at
>
>     http://bioperl.org/Core/external.shtml
>
>     Enjoy the rest of bioperl, which you can use after going 'make install'
>
> Writing Makefile for Bio
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu