[Bioperl-l] Re: [GMOD-devel] RPMs for bioperl

[Jason Stajich]

srsperl is only for people with srs you should have it be ignored.

if you are using cpan2rpm I would tell it to ignore certain 
dependancies. When I built rpms for our internal machines I just had it 
ignore the non-essential ones like Ace, etc.

-jason
On Jan 26, 2005, at 1:27 AM, Allen Day wrote:

> Hi,
>
> I've put together a set of RPMs for Bioperl, Bioperl-DB, Bioperl-Run, 
> and
> GBrowse.  It's still a work in progress, but you can see the current 
> state
> here:
>   http://sumo.genetics.ucla.edu/~allenday/flute/bioperl-1.5/i686/
> There are some related directories rooted here:
>   http://sumo.genetics.ucla.edu/~allenday/flute/
>
> The RPMs don't install clean.  This is because I'm using an automated 
> tool
> to build the RPMs, and it looks through each downloaded tarball from 
> CPAN
> to see what that tarball depends on.  Sometimes there are dependencies 
> on
> libraries that don't exist on CPAN, or might be altogether 
> non-existent.
> These are the problem libraries and binaries:
>
> % rpm -Uvh --test *.rpm
> error: Failed dependencies:
>         perl(Ace::Browser::LocalSiteDefs) is needed by 
> perl-AcePerl-1.87-allenday
>         perl(Bio::Das::ProServer::SourceHydra) is needed by 
> perl-Bio-Das-0.99-allenday
>         perl(IndexSupport) is needed by perl-Bio-Das-0.99-allenday
>         perl(srsperl) is needed by perl-bioperl-1.5.0-allenday
>         perl(Bio::DB::BioDB) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(Bio::DB::Query::BioQuery) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(GuessDirectories) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(MOBY::Client::Central) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(MOBY::Client::Service) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(MOBY::CommonSubs) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(MOBY::MobyXMLConstants) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(PPM::Archive) is needed by 
> perl-Generic-Genome-Browser-1.62-allenday
>         perl(MQClient::MQSeries) is needed by 
> perl-SOAP-Lite-0.60-allenday
>         perl(MQSeries) is needed by perl-SOAP-Lite-0.60-allenday
>         perl(MQSeries::Message) is needed by 
> perl-SOAP-Lite-0.60-allenday
>         perl(MQSeries::Queue) is needed by perl-SOAP-Lite-0.60-allenday
>         perl(MQSeries::QueueManager) is needed by 
> perl-SOAP-Lite-0.60-allenday
>         /bin/perl is needed by perl-Tk-804.027-allenday
>         /usr/local/bin/perl is needed by perl-Tk-804.027-allenday
>         perl(Tk::LabRadio) is needed by perl-Tk-804.027-allenday
>         perl(Tk::TextReindex) is needed by perl-Tk-804.027-allenday
>         perl(XML::LibXML) >= 1.57 is needed by 
> perl-XML-LibXSLT-1.57-allenday
>         perl(XML::SAX::PurePerl::DTDDecls) is needed by 
> perl-XML-SAX-0.12-allenday
>         perl(XML::SAX::PurePerl::DocType) is needed by 
> perl-XML-SAX-0.12-allenday
>         perl(XML::SAX::PurePerl::EncodingDetect) is needed by 
> perl-XML-SAX-0.12-allenday
>         perl(XML::SAX::PurePerl::XMLDecl) is needed by 
> perl-XML-SAX-0.12-allenday
>
> Lincoln, I'm guessing you can help me with:
>
> * Ace::Browser::LocalSiteDefs
> * Bio::Das::ProServer::SourceHydra
> * GuessDirectories
> * IndexSupport
> * MOBY::*
>
> Hilmar, do you know about:
>
> * Bio::DB::BioDB
> * Bio::DB::Query::BioQuery
>
> I'm sure someone on this list knows where to get
>
> * srsperl
> * PPM::Archive
>
> If anyone can shed light on where any of these libraries can be found, 
> I'd
> appreciate it.  Thanks.
>
> -Allen
>
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/