Saturday, 10 April 2010

perl Bio::Graphics module dependencies in ubuntu 9.04

Following my previous posts I am puting this here for future googling ;-).

These are the failed dependencies that I had when I tried the CPAN install Lincon Stein's Bio::Graphic (in a fresh installed linux box). I need to say that I have installed Bioperl and Bio::Graphics in all my developing machines and laptops many times and usually it works without problems at the first go, but this is because I usually had a lot of things already installed.

But now when I have run CPAN install Bio::Graphics in a clean box I have had a lot of 'expected' dependence issues:

Failed during this command:
MSERGEANT/XML-Parser-2.36.tar.gz : make NO
MKUTTER/SOAP-Lite-0.710.10.tar.gz : make_test NO
LBROCARD/GraphViz-2.04.tar.gz : writemakefile NO '/home/pablo/localperl/bin/perl Makefile.PL' returned status 512
MIROD/XML-Twig-3.32.tar.gz : make_test NO
PMQS/DB_File-1.820.tar.gz : make NO
KMACLEOD/libxml-perl-0.08.tar.gz : make_test NO
TJMATHER/XML-DOM-1.44.tar.gz : make_test NO
MIROD/XML-DOM-XPath-0.14.tar.gz : make_test NO
CJFIELDS/BioPerl-1.6.1.tar.gz : make_test NO
LDS/GD-2.44.tar.gz : writemakefile NO '/home/pablo/localperl/bin/perl Makefile.PL' returned status 512
LDS/Bio-Graphics-1.994.tar.gz : make_test NO

Then I needed to install this:

* sudo aptitude install
- libgd2-xpm-dev # gd for GD. I don't know the difference between xpm and noxpm but anyway
- libexpat-dev # expat for XML::Parser
- graphviz graphviz-dev graphviz-doc libgraphviz-dev graphviz-cairo # for GraphViz
- libdb4.6-dev # for DB_File (The headers for 4.7 were also available but I had 4.6 installed)

And this CPAN modules in this order:

- install IPC::Run # for GraphViz and other modules
- install DB_File # used by several modules so it better to install it first
- install XML::parser
- install GraphViz
- install GD
- install CJFIELDS/BioPerl-1.6.1.tar.gz

And then I was able to install Bio::Graphics

The only caveats here are that you should know that you need the expat for XML, IPC::Run for GraphViz dependency and that DB_File uses the Berkeley db headers (that I needed to google for finding the package that contains them).

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