[Bioperl-l] bioperl easy way installation using cpan

Scott Cain scott at scottcain.net
Mon Oct 18 13:26:53 EDT 2010


Hi Elena,

I would suggest that you answer the question about installing optional
prerequisites with a "no"; I think that will eliminate the circular
dependency problem.  Of course the only problem is if you need
Bio-ASN1-EntrezGene, but even if you do, you can probably install it
after the BioPerl install completes.

Scott


On Mon, Oct 18, 2010 at 10:33 AM, Cristiano Elena
<e.cristiano at dkfz-heidelberg.de> wrote:
> Hi,
> I am a beginner and i am trying to install bioperl via CPAN following the instructions on wiki.
> i have a leopard mac 10.6 and perl version 5.10 i have X11 and i also installed fink (but the installation of bioperl wasn't successful trough fink either).
>
> the error that i got at the end of the installation via CPAN is the following:
>
>  SHAWNPW/PostScript-0.06.tar.gz
>  /usr/bin/make install  -- OK
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>  Has already been unwrapped into directory /Users/ecristiano/.cpan/build/BioPerl-1.6.1-66fecx
> Could not make: cannot resolve circular dependency
> Warning (usually harmless): 'YAML' not installed, will not store persistent state
> Running Build test
>  Can't test without successful make
> Running Build install
>  Make had returned bad status, install seems impossible
> Could not read '/Users/ecristiano/.cpan/build/GraphViz-2.04-f7G5nl/META.yml'. Falling back to other methods to determine prerequisites
> Failed during this command:
>  MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz: make NO cannot resolve circular dependency
>  CJFIELDS/BioPerl-1.6.1.tar.gz                : make NO cannot resolve circular dependency
>  LBROCARD/GraphViz-2.04.tar.gz                : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
>
>
> thanks in advance
>
>
>
> Elena
>
>
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>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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