Package 'Cummerbund' Is Not Available

Question

[groundcover]

I'm trying to install the package cummeRbund in R as shown below but I keep getting the error shown below.

Does anyone know what could be going wrong? Or is there a way I can install it from source without using that biocLite.R command? (I'm pretty new to R)

(I also get the exact same results when I launch R with the --vanilla option)

[root@f01u01 bin]# ./R

R version 2.9.1 (2009-06-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

source('http://www.bioconductor.org/biocLite.R')
biocLite('cummeRbund')
Using R version 2.9.1, biocinstall version 2.4.13.
Installing Bioconductor version 2.4 packages:
[1] "cummeRbund"
Please wait...

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package 'cummeRbund' is not available

[Sukhi Singh]

Update your R, it will solve the problem, its quite old.

Answer 1

[Ben]

I'd guess it's just that you have an old version of R installed, try updating to the newest (2.15.2) or at least 2.14.

Aside: is R not installed somewhere in your path? And is there any reason you're running normal programs as root?

[groundcover]

Yes, normal users don't have permission to install libraries. We have several R installs so normal users get their path set to the version of R they've chosen. I'll try a newer version though.

[Neilfws]

cummeRbund is supposed to require R >= 2.7.0 so I'm not sure why 2.9 would be an issue (although 2.9 is very old and you should upgrade). Is "package 'cummeRbund' is not available" the complete error message? Are you sure it does not say "is not available for R ..." where "..." is a version?

[Ben]

Could have been dependencies or OS... but yeah it's not ideal that biocLite is less informative than install.packages

[shigeta]

I'm currently trying to install cummeRbund and bioconductor's telling me I need to upgrade R to 2.13.0 ,but cummeRbund install throws an error saying its not compatible beyond 2.12.0. Seems like cummeRbund is not currently available.

[Neilfws]

There is a current version for 2.13 right here. Suspect the issue is with your setup.