[BioC] Rgraphviz on Fedora Core 6

[Seth Falcon]

"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