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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 on Teton across the clusters and across disciplines and the 100s of libraries being used.
Using
On Teton, we have built a version of R 4 r/r4.0.5-py27 with a selection of common libraries pre-installed.
This can be loaded by:
...
.
Listing Packages
Since this build has > 500 libraries, there are too many to individually list here.
...
| Code Block |
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> 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:
Conflicting Versions of Libraries: libPath()
Requesting a Package to be Included:
We are looking to review the base version of R and list of packages on a semi-regular basis, so if there is a useful package that is being widely used across a group then we can consider adding it to the package list. Please send a request to the arcc-help@uwyo.edu email list. Please be aware that we can not always install a package due to conflicting dependencies issues with other packages and low level system level requirements. In these cases we can look at building a bespoke container for this purposebe aware of conflicting libPaths that you might have installed locally. See the section on our general R Packages/Libraries page for more details.