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