R help - May 2011 - issue with graph package in using RBGL -‘'graph' is not a valid installed package’"

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?".

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

On 11.05.2011 16:51, 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/).

They are removed in order not to double host them. In the first place, 
both are BioConductor packages and you can get them using 
install.packages(c("graph", RBGL"), dependencies=TRUE)) after 
chooseBioCmirror() and setRepositories().



> 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?".
You downloaded the source package (in a tar.gz file) but used the 
mechanism to install a binary package (in a zip file). Either learn how 
to install from sources (see manual R Installation and Administration) 
or use BioConductor mirrors.

Uwe Ligges

> 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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.