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Question: Package RnBeads not available for R 3.1.2?
0
gravatar for bmreilly
2.4 years ago by
bmreilly0
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:


source("http://bioconductor.org/biocLite.R")

biocLite("RnBeads")


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()
Repositories

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


I think this is correct though?

any help is appreciated.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by bmreilly0
2
gravatar for Dan Tenenbaum
2.4 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 2.4 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 2.4 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 2.4 years ago by Dan Tenenbaum ♦♦ 8.2k

Great, thanks for the tip!

ADD REPLYlink written 2.3 years ago by bmreilly0
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