you will need librdf.so and LD_LIBRARY_PATH suitably set.  i have succeeded
with
librdf 1.0.8 on a centos system.  building librdf 1.0.9 from svn source
requires various gnome
and docbook facilities that i have had trouble with.  the point is that,
like graphviz or XML,
the Rredland package is not self-contained -- you need an external library.

On Thu, Apr 30, 2009 at 12:34 PM, Paul Shannon
<pshannon@systemsbiology.org>wrote:

> Vince and Patrick,
>
> Thanks to you both for your replies.
>
> I propose to install Rredland on a linux box, and try out the idea of using
> it to obtain networks from NCI.  That ought to work, right? -- Rredland is
> known to work when built from source on linux?
>
> If NCI proves to be a good source for cancer-related pathways, then maybe
> that would justify including mac.binary.leopard builds at some time in the
> future.
>
>  - Paul
>
>
> On Apr 29, 2009, at 7:42 PM, Vincent Carey wrote:
>
>  for what it's worth, librdf has supported sqlite stores for some time.  we
>> might consider dropping
>> the requirement for the BDB back end and use sqlite henceforth.  if i knew
>> there were users
>> i would explore this; a caveat is that the redland examples of the sqlite
>> interface were not
>> very clear when i last checked.
>>
>> On Wed, Apr 29, 2009 at 9:25 PM, Patrick Aboyoun <paboyoun@fhcrc.org>
>> wrote:
>> Paul,
>> 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 this.
>>
>>
>> Patrick
>>
>>
>>
>> Quoting Paul Shannon <pshannon@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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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>> _______________________________________________
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>>
>>
>>
>> --
>> Vincent Carey, PhD
>> Biostatistics, Channing Lab
>> 617 525 2265
>>
>
>


-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265

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