[R] issue with graph package in using RBGL -‘'graph' is not a valid installed package’"

[Duncan Murdoch]

On 11/05/2011 10:51 AM, joe j wrote:
> Dear all,
>
> I am trying to run the function "lambdaSets" using the package "RBGL".
> This package uses another package "graph" which has been removed from
> the CRAN repository, but is available at the archive
> (http://cran.r-project.org/src/contrib/Archive/graph/).
>
> I installed the package from the R menu at "install packages from
> local zip files" (after downloading the "graph_1.30.0.tar.gz" file,
> unzipping it and making it a zip file; gz is not recognized by R.). I
> get no warning here so I assumed installation went well. However, when
> I type "require(RBGL)" I get the error message that: "Failed with
> error:  ‘'graph' is not a valid installed package’".

Installing a package is not that simple.  R does various processing when 
taking the source tar.gz file and producing the binary image that it 
puts in the .zip.  You would need to run

R CMD INSTALL graph_1.30.0.tar.gz

to do the install, but you probably don't have the tools installed to 
get this to work.

However, graph is available on the Bioconductor web site, so if you 
select "BioC software" as a repository selection, the regular menu entry 
for installing packages should work.  I just tested it on Windows, which 
I assume you're using (since other platforms don't use .zip).

Duncan Murdoch
> I am using R version 2.12.2 (2011-2-25). I am a new user so your
> advice would be of great help.
>
> Best wishes,
> Joe
>
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