Question: Package RnBeads not available for R 3.1.2?
gravatar for bmreilly
3.4 years ago by
United States
bmreilly0 wrote:

I am having trouble installing the package 'RnBeads' on my institutions cluster.

The cluster is running R version 3.1.2. and Bioconductor 3.0, BiocInstaller 1.16.5.

when I do:



I keep getting the error:

Warning message:
package ‘RnBeads’ is not available (for R version 3.1.2)

I have not found a way to get around this, and the RnBeads bioconductor page says the package only depends on R >3.0.0, so I'm not sure why it would not be available in R 3.1.2?

I have checked if it is because I had not set my repositories correctly:

> setRepositories()

1: + CRAN
2: + BioC software
3: + BioC annotation
4: + BioC experiment
5: + BioC extra
6: + CRAN (extras)
7:   Omegahat
8:   R-Forge

I think this is correct though?

any help is appreciated.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by bmreilly0
gravatar for Dan Tenenbaum
3.4 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

The RnBeads landing page says that RnBeads was added in Bioconductor 3.1 which is the current release version and runs on R-3.2.

So you can't run it on your cluster unless you update it to run R-3.2.


ADD COMMENTlink written 3.4 years ago by Dan Tenenbaum ♦♦ 8.2k

Okay, thanks for pointing that out. 

Was I misinterpreting the dependencies table on the landing page?  Why does the dependencies table show that RnBeads depends on =>R-3.0.0 when it will only run on 3.2?  Should I just infer the R version based on the BIoconductor version in the future?

ADD REPLYlink written 3.4 years ago by bmreilly0

There is a line on the landing page that says "In Bioconductor Since". That's what you want to go by.

We currently encourage (via BiocCheck) package maintainers to update their R dependency to an appropriate value but "In Bioconductor Since" is the canonical place to find out when (in which version) a package was added to Bioconductor (and it won't be available for earlier versions).

ADD REPLYlink written 3.4 years ago by Dan Tenenbaum ♦♦ 8.2k

Great, thanks for the tip!

ADD REPLYlink written 3.4 years ago by bmreilly0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 242 users visited in the last hour