[BioC] Rredland installation difficulties

Patrick Aboyoun paboyoun at fhcrc.org
Thu Apr 30 03:25:23 CEST 2009

We currently don't support Rredland in a mac.binary.leopard format  
because we don't have the infrastructure in place to support it on the  
build machine. Since we build universal binaries (i386, x86_64, ppc)  
on Mac OS X Leopard we usually have to build 3rd party libraries  
ourselves, unless generous people in the user community build them for  
us. (Thanks Gtk+ team!) With Rredland we need to install both redland  
and Berkeley DB on our build machine. I have redland in place, but  
need to do some research getting Berkeley DB installed. If we do move  
to support Rredland in a mac.leopard.binary form, it will more than  
likely be with custom builds with libraries located in /usr/local, not  
/opt/local as darwin ports likes to use, just as the Tiger build is  
structured. Have you tried to install the package from source? If so  
what results have you had?

Thanks for the tip on the misdirected link. I suspect the Reference  
Manual wasn't built properly and this the result. I'll look to correct  


Quoting Paul Shannon <pshannon at systemsbiology.org>:

> I wish to read BioPAX level 2 pathway files from the National Cancer
> Institute's 'Pathway Interaction Database'.  Rredland was recommended
> to me which looks looks very promising.  Perhaps these pathways can
> even be expressed as a bioc graph...
> I have enountered some of problems, leading to these questions and comments:
> 1) Lacking librdf, I used darwin ports to install it on my MacBook
> (Leopard) laptop.  This installed lots of libraries to /opt/local/lib.
> Rredland seems to want dynamic libraries in /usr/local/lib.  Is this a
> mac os x tiger/leopard difference?   Do I run into this because I used
> the Tiger binary, in the absence of a Leopard binary?  Is a Leopard
> binary planned for the future?  Shall I try to build from source?
> 2) (minor) The 'Reference Manual' link at
> http://www.bioconductor.org/packages/release/bioc/html/Rredland.html
> points to       http://www.bioconductor.org/packages/release/bioc/,
> rather than to a document.
> Thanks!
>  - Paul
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