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

[Allen Day]

i can do that, but i'd rather just include all optional modules are 
prerequisites rather than making a custom specfile.  any idea where i can 
find srsperl?  a google search didn't turn anything up.

-allen

On Wed, 26 Jan 2005, Jason Stajich wrote:

> 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/
>