[Bioperl-l] bioperl::db

Bernd Mueller bernd at kirx.de
Sun Apr 29 18:57:53 EDT 2007

Hello list,

I figured out my problem. Actually it was because of problems in the 
versioning of bioperl. It is described to figure out the available 
versions of bioperl in CPAN but afterwards it is described to install a 
much higher version wich is not listed as distribution in CPAN. So it 
works fine now. Thanks anyway. Proficiency in reading results in success ;-)

But I have another question: Does anyone know how to retrieve free 
fulltext documents with EUtilities from Pubmed Central? All my queries 
result in a corpora of free and non-free articles.

Thanks and regards,


Bernd Mueller wrote:
> Hi,
> I followed those instructions on bioperl.org for installing bioperl via 
> cpan. But actually it is impossible for me to install the bioperl::db 
> module.
> How does this work?
> Moreover none of these Birney distribution are installable on my system. 
> After typing cpan> install BIRNEY/bioperl-x.x.x.x, the tests always 
> fail. So I have to install the CRAFFI bundle but it does not seem that 
> Bio::DB module is included in this bundle because my programs using that 
> module do not work.
> Help would be appreciated :)
> Cheers,
> Bernd
> Appendix:
> cpan[6]> d /bioperl/
> Distribution    BIRNEY/bioperl-1.2.1.tar.gz
> Distribution    BIRNEY/bioperl-1.2.2.tar.gz
> Distribution    BIRNEY/bioperl-1.2.3.tar.gz
> Distribution    BIRNEY/bioperl-1.2.tar.gz
> Distribution    BIRNEY/bioperl-1.4.tar.gz
> Distribution    BIRNEY/bioperl-db-0.1.tar.gz
> Distribution    BIRNEY/bioperl-ext-1.4.tar.gz
> Distribution    BIRNEY/bioperl-gui-0.7.tar.gz
> Distribution    BIRNEY/bioperl-run-1.2.2.tar.gz
> Distribution    BIRNEY/bioperl-run-1.4.tar.gz
> Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
> Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
> 12 items found

Bernd Mueller
phone: +49 179 2336692
email: bernd at kirx.de

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