[Bioperl-l] bioperl easy way installation using cpan

Chris Fields cjfields at illinois.edu
Mon Oct 18 13:37:02 EDT 2010


Agreed.  Unfortunately, this is an issue that has repeatedly popped up.  The best way I can think of to solve it is to remove Bio::ASN1::EntrezGene 'recommends' from Build.PL file, manually check for it's presence, and indicate the procedure for installing (basically post-bioperl install).

chris

On Oct 18, 2010, at 12:26 PM, Scott Cain wrote:

> 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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>> Bioperl-l at lists.open-bio.org
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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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