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R is a free software environment for statistical computing and graphics.
| Version | module name | build | notes |
|---|
| 4.0.3 | r/4.0.3 | SPACK using gcc 8.3.1 | optimized for avx, avx2 and avx512 |
| 4.0.5 | conda/r | Conda packages | Load anaconda3/2020.07 first |
| 4.1.1 | conda/spark | Conda packages | Load anaconda3/2020.07 first.
For use with Apache Spark |
Seminar Slides
Installed Packages
R packages are built using SPACK optimized for the underlying CPU architecture or binary installs using Conda. Applications built by RC staff that are dependent on R use the SPACK built R packages.
Package List
Package | 4.0.3 SPACK | 4.0.5 Conda |
|---|
abind |
| 1.4-5 |
acepack | 1.4.1 |
|
amap | 0.8-17 |
|
animation | 2.6 |
|
annotate | 1.62.0 |
|
AnnotationDbi | 1.46.1 |
|
ape | 5.3 |
|
argparse | 2.0.1 |
|
askpass | 1.1 | 1.1 |
assertthat | 0.2.1 | 0.2.1 |
backports | 1.1.4 | 1.4.0 |
base | 4.0.3 | 4.0.5 |
base64enc | 0.1-3 | 0.1-3 |
BBmisc | 1.11 |
|
BH | 1.69.0-1 |
|
BiasedUrn | 1.07 |
|
bibtex | 0.4.2 |
|
bigmemory | 4.5.36 |
|
bigmemory.sri | 0.1.3 |
|
Biobase | 2.44.0 |
|
BiocGenerics | 0.34.0 |
|
BiocManager | 1.30.10 |
|
BiocParallel | 1.18.1 |
|
biomaRt | 2.40.5 |
|
Biostrings | 2.52.0 |
|
bit | 1.1-14 | 4.0.4 |
bit64 | 0.9-7 | 4.0.5 |
bitops | 1.0-6 |
|
blob | 1.2.0 | 1.2.2 |
boot | 1.3-27 | 1.3-28 |
brew | 1.0-6 |
|
brio |
| 1.1.3 |
broom | 0.5.2 | 0.7.10 |
bslib |
| 0.3.1 |
cachem |
| 1.0.6 |
callr | 3.4.3 | 3.7.0 |
car |
| 3.0-12 |
carData |
| 3.0-4 |
caret | 6.0-84 | 6.0-90 |
caTools | 1.17.1.2 |
|
cellranger | 1.1.0 | 1.1.0 |
checkmate | 1.9.4 |
|
chron | 2.3-53 |
|
class | 7.3-18 | 7.3-19 |
cli | 2.0.2 | 3.1.0 |
clipr | 0.7.0 | 0.7.1 |
cluster | 2.1.1 | 2.1.2 |
clusterGeneration | 1.3.4 |
|
coda | 0.19-3 |
|
codetools | 0.2-18 | 0.2-18 |
colorspace | 1.4-1 | 2.0-2 |
combinat | 0.0-8 |
|
commonmark | 1.7 | 1.7 |
compiler | 4.0.3 | 4.0.5 |
config |
| 0.3.1 |
conquer |
| 1.2.1 |
corrplot |
| 0.92 |
covr | 3.5.0 |
|
cowplot | 1.0.0 | 1.1.1 |
cpp11 |
| 0.4.2 |
crayon | 1.3.4 | 1.4.2 |
crosstalk | 1.0.0 | 1.2.0 |
crul |
| 1.2.0 |
ctc | 1.58.0 |
|
curl | 4.3 | 4.3.2 |
data.table | 1.12.8 | 1.14.2 |
datasets | 4.0.3 | 4.0.5 |
DBI | 1.1.0 | 1.1.1 |
dbplyr | 1.4.2 | 2.1.1 |
DelayedArray | 0.10.0 |
|
dendextend | 1.12.0 |
|
desc | 1.2.0 | 1.4.0 |
DESeq2 | 1.24.0 |
|
devtools | 2.3.0 |
|
DEXSeq | 1.36.0 |
|
diffobj |
| 0.3.5 |
digest | 0.6.25 | 0.6.29 |
doParallel | 1.0.15 |
|
dplyr | 0.8.3 | 1.0.7 |
dqrng | 0.2.1 |
|
DT | 0.13 | 0.20 |
dtplyr |
| 1.2.0 |
dygraphs | 1.1.1.6 | 1.1.1.6 |
e1071 |
| 1.7-9 |
edgeR | 3.26.8 |
|
ellipsis | 0.3.0 | 0.3.2 |
evaluate | 0.14 | 0.14 |
expm | 0.999-4 |
|
fansi | 0.4.0 | 0.5.0 |
farver |
| 2.1.0 |
fastcluster | 1.1.25 |
|
fastmap |
| 1.1.0 |
fastmatch | 1.1-0 |
|
findpython | 1.0.5 |
|
fitdistrplus | 1.0-14 |
|
flexdashboard |
| 0.5.2 |
FNN | 1.1.3 |
|
fontawesome |
| 0.2.2 |
forcats | 0.4.0 | 0.5.1 |
foreach | 1.4.7 | 1.5.1 |
foreign | 0.8-81 | 0.8-81 |
forge |
| 0.2.0 |
formatR | 1.7 | 1.11 |
Formula | 1.2-3 |
|
fs | 1.3.1 | 1.5.2 |
futile.logger | 1.4.3 |
|
futile.options | 1.0.1 |
|
future | 1.14.0 | 1.23.0 |
future.apply | 1.3.0 | 1.8.1 |
gargle |
| 1.2.0 |
gbRd | 0.4-11 |
|
gdata | 2.18.0 |
|
gdtools |
| 0.2.3 |
genefilter | 1.72.1 |
|
geneLenDataBase | 1.20.0 |
|
geneplotter | 1.62.0 |
|
generics | 0.0.2 | 0.1.1 |
GenomeInfoDb | 1.20.0 |
|
GenomeInfoDbData | 1.2.1 |
|
GenomicAlignments | 1.20.1 |
|
GenomicFeatures | 1.36.4 |
|
GenomicRanges | 1.36.1 |
|
ggdendro | 0.1-20 |
|
ggplot2 | 3.2.0 | 3.3.5 |
ggpubr |
| 0.4.0 |
ggrepel | 0.8.1 | 0.9.1 |
ggridges | 0.5.1 |
|
ggsci |
| 2.9 |
ggsignif |
| 0.6.3 |
gh | 1.1.0 |
|
gistr | 0.4.2 | 0.9.0 |
git2r | 0.27.1 |
|
Glimma | 1.12.0 |
|
glmnet |
| 4.1-2 |
globals | 0.12.4 | 0.14.0 |
glue | 1.4.1 | 1.5.1 |
gmodels | 2.18.1 |
|
GO.db | 3.4.1 |
|
googledrive |
| 2.0.0 |
googlesheets4 |
| 1.0.0 |
GOplot | 1.0.2 |
|
goseq | 1.36.0 |
|
gower | 0.2.1 | 0.2.2 |
gplots | 3.0.1.1 |
|
graphics | 4.0.3 | 4.0.5 |
grDevices | 4.0.3 | 4.0.5 |
grid | 4.0.3 | 4.0.5 |
gridExtra | 2.3 | 2.3 |
gsubfn | 0.7 |
|
gtable | 0.3.0 | 0.3.0 |
gtools | 3.8.1 |
|
haven | 2.1.1 | 2.4.3 |
hdf5r | 1.2.0 |
|
here |
| 1.0.1 |
hexbin | 1.27.3 | 1.28.2 |
highr | 0.8 | 0.9 |
Hmisc | 4.4-0 |
|
hms | 0.5.0 | 1.1.1 |
htmlTable | 1.13.1 |
|
htmltools | 0.3.6 | 0.5.2 |
htmlwidgets | 1.3 | 1.5.4 |
httpcode |
| 0.3.0 |
httpuv | 1.5.1 | 1.6.3 |
httr | 1.4.1 | 1.4.2 |
hwriter | 1.3.2 |
|
ica | 1.0-2 |
|
ids |
| 1.0.1 |
igraph | 1.2.4.1 |
|
ini | 0.3.1 |
|
inline | 0.3.15 |
|
ipred | 0.9-9 | 0.9-12 |
IRanges | 2.22.2 |
|
IRdisplay |
| 1.0 |
IRkernel |
| 1.2 |
irlba | 2.3.3 |
|
isoband |
| 0.2.5 |
iterators | 1.0.12 | 1.0.13 |
janitor | 1.2.0 |
|
jquerylib |
| 0.1.4 |
jsonlite | 1.6.1 | 1.7.2 |
kableExtra |
| 1.3.4 |
KernSmooth | 2.23-18 | 2.23-20 |
knitr | 1.28 | 1.36 |
labeling | 0.3 | 0.4.2 |
lambda.r | 1.2.3 |
|
later | 0.8.0 | 1.2.0 |
lattice | 0.20-41 | 0.20-45 |
latticeExtra | 0.6-28 |
|
lava | 1.6.6 | 1.6.10 |
lazyeval | 0.2.2 | 0.2.2 |
leiden | 0.3.1 |
|
lifecycle |
| 1.0.1 |
limma | 3.40.6 |
|
listenv | 0.7.0 | 0.8.0 |
lme4 | 1.1-21 | 1.1-27.1 |
lmtest | 0.9-37 |
|
lobstr |
| 1.1.1 |
locfit | 1.5-9.1 |
|
loo | 2.1.0 |
|
lsei | 1.2-0 |
|
lubridate | 1.7.4 | 1.8.0 |
magick | 2.1 |
|
magrittr | 1.5 | 2.0.1 |
maps | 3.3.0 | 3.4.0 |
maptools |
| 1.1-2 |
markdown | 1.1 | 1.1 |
MASS | 7.3-53.1 | 7.3-54 |
Matrix | 1.3-2 | 1.3-4 |
MatrixModels |
| 0.5-0 |
matrixStats | 0.55.0 | 0.61.0 |
memoise | 1.1.0 |
|
metap | 1.1 |
|
methods | 4.0.3 | 4.0.5 |
mgcv | 1.8-34 | 1.8-38 |
mime | 0.7 | 0.12 |
minqa | 1.2.4 | 1.2.4 |
mlr | 2.15.0 |
|
mnormt | 1.5-5 |
|
ModelMetrics | 1.2.2 | 1.2.2.2 |
modelr | 0.1.5 | 0.1.8 |
multtest | 2.40.0 |
|
munsell | 0.5.0 | 0.5.0 |
ncdf4 | 1.16.1 |
|
nlme | 3.1-152 | 3.1-150 |
nloptr | 1.2.1 | 1.2.2.2 |
nnet | 7.3-15 | 7.3-16 |
npsurv | 0.4-0 |
|
numDeriv | 2016.8-1.1 | 2016.8-1.1 |
openssl | 1.4.1 | 1.4.5 |
openxlsx | 4.1.0.1 | 4.2.4 |
pacman | 0.5.1 |
|
parallel | 4.0.3 | 4.0.5 |
parallelly |
| 1.29.0 |
parallelMap | 1.4 |
|
ParamHelpers | 1.12 |
|
pbapply | 1.4-1 |
|
pbdZMQ |
| 0.3-6 |
pbkrtest |
| 0.5.1 |
phangorn | 2.5.5 |
|
phytools | 0.6-99 |
|
pillar | 1.4.2 | 1.6.4 |
pkgbuild | 1.0.8 |
|
pkgconfig | 2.0.2 | 2.0.3 |
pkgload | 1.0.2 | 1.2.4 |
plogr | 0.2.0 |
|
plotly | 4.9.0 | 4.10.0 |
plotrix | 3.7-6 |
|
plyr | 1.8.4 | 1.8.6 |
png | 0.1-7 | 0.1-7 |
polynom |
| 1.4-0 |
praise | 1.0.0 | 1.0.0 |
prettyunits | 1.0.2 | 1.1.1 |
pROC |
| 1.18.0 |
processx | 3.4.1 | 3.5.2 |
prodlim | 2018.04.18 | 2019.11.13 |
progress | 1.2.2 | 1.2.2 |
progressr |
| 0.9.0 |
promises | 1.0.1 | 1.2.0.1 |
proto | 1.0.0 |
|
proxy |
| 0.4-26 |
pryr | 0.1.4 | 0.1.5 |
ps | 1.3.0 | 1.6.0 |
purrr | 0.3.4 | 0.3.4 |
quadprog | 1.5-7 |
|
quantmod | 0.4-15 | 0.4.18 |
quantreg |
| 5.86 |
qvalue | 2.16.0 |
|
R.methodsS3 | 1.7.1 |
|
R.oo | 1.23.0 |
|
R.utils | 2.9.0 |
|
r2d3 |
| 0.2.5 |
R6 | 2.4.0 | 2.5.1 |
randomForest | 4.6-14 | 4.6-14 |
RANN | 2.6.1 |
|
rappdirs | 0.3.1 | 0.3.3 |
rbokeh | 0.5.0 | 0.5.2 |
rcmdcheck | 1.3.3 |
|
RColorBrewer | 1.1-2 | 1.1-2 |
Rcpp | 1.0.4.6 | 1.0.7 |
RcppAnnoy | 0.0.12 |
|
RcppArmadillo | 0.9.600.4.0 | 0.10.7.3.0 |
RcppEigen | 0.3.3.5.0 | 0.3.3.9.1 |
RcppParallel | 4.4.3 |
|
RcppProgress | 0.4.1 |
|
RCurl | 1.98-1.2 |
|
Rdpack | 0.11-0 |
|
readr | 1.3.1 | 2.1.1 |
readxl | 1.3.1 | 1.3.1 |
recipes | 0.1.6 | 0.1.17 |
rematch | 1.0.1 | 1.0.1 |
rematch2 | 2.1.2 | 2.1.2 |
remotes | 2.1.1 |
|
repr |
| 1.1.3 |
reprex | 0.3.0 | 2.0.1 |
reshape2 | 1.4.3 | 1.4.4 |
reticulate | 1.15 | 1.22 |
rex | 1.1.2 |
|
rhdf5 | 2.28.1 |
|
Rhdf5lib | 1.6.3 |
|
Rhtslib | 1.18.1 |
|
rio |
| 0.5.29 |
rjson |
| 0.2.20 |
rlang | 0.4.6 | 0.4.12 |
rmarkdown | 1.14 | 2.11 |
ROCR | 1.0-7 |
|
ROTS | 1.12.0 |
|
roxygen2 | 7.1.0 |
|
rpart | 4.1-15 | 4.1-15 |
RPostgreSQL | 0.6-2 |
|
rprojroot | 1.3-2 | 2.0.2 |
Rsamtools | 2.2.1 |
|
RSpectra | 0.15-0 |
|
RSQLite | 2.1.2 |
|
rstan | 2.19.2 |
|
rstatix |
| 0.7.0 |
rstudioapi | 0.11 | 0.13 |
rsvd | 1.0.2 |
|
rtracklayer | 1.44.4 |
|
Rtsne | 0.15 |
|
rversions | 2.0.1 |
|
rvest | 0.3.4 | 1.0.2 |
S4Vectors | 0.26.1 |
|
sass |
| 0.4.0 |
scales | 1.0.0 | 1.1.1 |
scatterplot3d | 0.3-41 |
|
sctransform | 0.2.0 |
|
SDMTools | 1.1-221.1 |
|
selectr | 0.4-1 | 0.4-2 |
sessioninfo | 1.1.1 |
|
Seurat | 3.1.0 |
|
shape |
| 1.4.6 |
shiny | 1.3.2 | 1.7.1 |
sitmo | 2.0.1 |
|
sm | 2.2-5.6 |
|
snakecase | 0.11.0 |
|
snow | 0.4-3 |
|
sourcetools | 0.1.7 | 0.1.7 |
sp |
| 1.4-6 |
sparklyr |
| 1.7.3 |
SparseM |
| 1.81 |
spatial |
| 7.3-14 |
splines | 4.0.3 | 4.0.5 |
splitstackshape | 1.4.8 |
|
sqldf | 0.4-11 |
|
SQUAREM | 2017.10-1 | 2021.1 |
StanHeaders | 2.18.1-10 |
|
statmod | 1.4.32 | 1.4.36 |
stats | 4.0.3 | 4.0.5 |
stats4 | 4.0.3 | 4.0.5 |
stringi | 1.4.3 | 1.7.6 |
stringr | 1.4.0 | 1.4.0 |
SummarizedExperiment | 1.18.2 |
|
survival | 3.2-7 | 3.2-13 |
svglite |
| 2.0.0 |
sys | 3.2 | 3.4 |
systemfonts |
| 1.0.3 |
tcltk | 4.0.3 | 4.0.5 |
testthat | 2.3.2 | 3.1.1 |
tibble | 2.1.3 | 3.1.6 |
tidyr | 0.8.3 | 1.1.4 |
tidyselect | 0.2.5 | 1.1.1 |
tidyverse | 1.2.1 | 1.3.1 |
timeDate | 3043.102 | 3043.102 |
tinytex | 0.15 | 0.35 |
tools | 4.0.3 | 4.0.5 |
triebeard |
| 0.3.0 |
tsne | 0.1-3 |
|
TTR | 0.23-4 | 0.24.2 |
tximport | 1.12.3 |
|
tximportData | 1.18.0 |
|
tzdb |
| 0.2.0 |
urltools |
| 1.7.3 |
usethis | 1.6.1 |
|
utf8 | 1.1.4 | 1.2.2 |
utils | 4.0.3 | 4.0.5 |
uuid |
| 1.0-3 |
uwot | 0.1.3 |
|
vctrs | 0.2.0 | 0.3.8 |
vioplot | 0.3.2 |
|
viridis | 0.5.1 |
|
viridisLite | 0.3.0 | 0.4.0 |
vroom |
| 1.5.7 |
waldo |
| 0.3.1 |
webshot |
| 0.5.2 |
whisker | 0.3-2 |
|
withr | 2.2.0 | 2.4.3 |
xfun | 0.8 | 0.28 |
XML | 3.98-1.20 |
|
xml2 | 1.3.2 | 1.3.3 |
xopen | 1.0.0 |
|
xtable | 1.8-4 | 1.8-4 |
xts | 0.11-2 | 0.12.1 |
XVector | 0.24.0 |
|
yaml | 2.2.0 | 2.2.1 |
zeallot | 0.1.0 |
|
zip | 2.0.3 | 2.2.0 |
zlibbioc | 1.30.0 |
|
zoo | 1.8-6 | 1.8-9 |
A comprehensive list of packages is available in the RStudio singularity images. Click here to view the list and instructions for using them outside RStudio.
How to install R packages?
A variety of R packages are installed however it is recommended that users install packages (newer and updated versions) in their own home directory.
Start interactive R session and install package using the command
install.packages('packagename')
Alternatively, you can add install.packages('packagename') within your R script. By default, R will try to install packages locally to ${HOME/x86_64-pc-linux-gnu-library. If you wish to use a different directory, then you need to set R_LIBS variable to point to that directory.
If you get an error installing packages locally, then use the command
install.packages('packagename',lib=Sys.getenv("R_LIBS"))
