R4.0.5 + Packages

1 Overview | 2 Using | 2.1 Listing Packages | 2.1.1 Package CNVRG: | 2.1.2 Issues:

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.