[BioC] Rgraphviz on Fedora Core 6

[Byron Wallace]

Thanks for all the help, it turned out to be a versioning issue. The
biocLite install method worked great once I swapped in bioconductor
1.9 with R 2.4.

On 1/31/07, Seth Falcon <sfalcon at fhcrc.org> wrote:
> "Byron Wallace" <Byron.Wallace at tufts.edu> writes:
>
> > Thank you so much! You were exactly right about bioconductor 1.8, and
> > I resolved the issue by installing graphviz 2.8.
>
> Not sure how this resolves your issues.
>
> > However, I've unfortunately encountered another issue. After I
> > succesfully install both 'graph_1.10.6' and 'Rgraphviz_1.10.0', I
> > start R (v 2.4) and attempt to run the install script to install all
> > the needed bioconductor packages. Here I get an error telling me
> > that the graph library is not installed (see below). I'm lost
> > because I the R CMD INSTALL for the graph library completes
> > successfully. Any insight here? Thank you again for your time.
>
> R has a default location for installing packages.  The -l argument to
> R CMD INSTALL will change the default.  The environment variable
> R_LIBS will also override.  From inside R, you can see what paths are
> searched for packages using .libPaths().  It seems likely that you
> have a mismatch in some way between where you installed and where R is
> looking.
>
> >> source("install.R")
> >> install()
> > checking for installed packages...
> > checking for graph: ...Error in install() :
> > ERROR: library graph not installed! install graph package before
> > running this script!
> > In addition: Warning message:
> > there is no package called 'graph' in: library(package, lib.loc =
> > lib.loc, character.only = TRUE, logical = TRUE,
>
> what's install.R?
>
> I would recommend using biocLite to install the packages you want:
>
> Start R and then...
>
> souce("http://bioconductor.org/biocLite.R")
> biocLite("Rgraphviz")
>
> + seth
>


-- 
- Byron C. Wallace