R4.0.5 + Packages
This page related to an older Teton cluster, but the process of identifying available packages still holds for other clusters.
Overview
ARCC is currently exploring ways to best support R users across the clusters and disciplines and the 100s of libraries being used.
Using
On Teton, we have built a version of r/r4.0.5-py27 with a selection of common libraries pre-installed.
Listing Packages
Since this build has > 500 libraries, there are too many to individually list here.
You can find if a package is available by:
> row.names(installed.packages())
[1] "annotate" "AnnotationDbi" "assertthat"
[4] "backports" "BH" "Biobase"
[7] "BiocGenerics" "BiocParallel" "BiocVersion"
[10] "Biostrings" "BSgenome" "Cairo"
[13] "callr" "checkmate" "chromVAR"
...Alternatively, if you wish to list a package per line, with its version, you can use:
> ip = as.data.frame(installed.packages()[,c(1,3:4)])
> ip = ip[is.na(ip$Priority),1:2,drop=FALSE]
> ip
Package Version
annotate annotate 1.68.0
AnnotationDbi AnnotationDbi 1.52.0
assertthat assertthat 0.2.1
backports backports 1.2.1
BH BH 1.75.0-0
Biobase Biobase 2.50.0
BiocGenerics BiocGenerics 0.36.1
BiocParallel BiocParallel 1.24.1
BiocVersion BiocVersion 3.12.0
Biostrings Biostrings 2.58.0
BSgenome BSgenome 1.58.0
Cairo Cairo 1.5-12.2
callr callr 3.5.1
...Package CNVRG:
One package that we currently haven’t explicitly installed is CNVRG. Since this is under active development we are waiting until it has a stable version, and then at this point we can look at packaging it with the others.
Issues:
Please be aware of conflicting libPaths that you might have installed locally. See the section on our general R Packages/Libraries page for more details.