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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> -- >> Vincent Carey, PhD >> Biostatistics, Channing Lab >> 617 525 2265 >> > > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265 [[alternative HTML version deleted]]