R

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
4.0.3	conda/r	Conda packages	Load anaconda3/2020.07 first

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	4.0.3 Conda
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	1.2.0
base	4.0.3	4.0.3
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
bit64	0.9-7
bitops	1.0-6
blob	1.2.0	1.2.1
boot	1.3-23	1.3-25
boot	1.3-27	1.3-25
brew	1.0-6
brio		1.1.0
broom	0.5.2	0.7.2
callr	3.4.3	3.5.1
caret	6.0-84	6.0-86
caTools	1.17.1.2
cellranger	1.1.0	1.1.0
checkmate	1.9.4
chron	2.3-53
class	7.3-15	7.3-17
cli	2.0.2	2.2.0
clipr	0.7.0	0.7.1
cluster	2.1.0	2.1.0
cluster	2.1.1	2.1.0
clusterGeneration	1.3.4
coda	0.19-3
codetools	0.2-16	0.2-18
codetools	0.2-18	0.2-18
colorspace	1.4-1	2.0-0
combinat	0.0-8
commonmark	1.7	1.7
compiler	4.0.3	4.0.3
covr	3.5.0
cowplot	1.0.0
cpp11		0.2.4
crayon	1.3.4	1.3.4
crosstalk	1.0.0	1.1.0.1
crul		1.0.0
ctc	1.58.0
curl	4.3	4.3
data.table	1.12.8	1.13.2
datasets	4.0.3	4.0.3
DBI	1.1.0	1.1.0
dbplyr	1.4.2	2.0.0
DelayedArray	0.10.0
dendextend	1.12.0
desc	1.2.0	1.2.0
DESeq2	1.24.0
devtools	2.3.0
DEXSeq	1.36.0
diffobj		0.3.2
digest	0.6.25	0.6.27
doParallel	1.0.15
dplyr	0.8.3	1.0.2
dqrng	0.2.1
DT	0.13	0.16
dygraphs	1.1.1.6	1.1.1.6
edgeR	3.26.8
ellipsis	0.3.0	0.3.1
evaluate	0.14	0.14
expm	0.999-4
fansi	0.4.0	0.4.1
farver		2.0.3
fastcluster	1.1.25
fastmap		1.0.1
fastmatch	1.1-0
findpython	1.0.5
fitdistrplus	1.0-14
flexdashboard		0.5.2
FNN	1.1.3
forcats	0.4.0	0.5.0
foreach	1.4.7	1.5.1
foreign	0.8-72	0.8-80
foreign	0.8-81	0.8-80
formatR	1.7	1.7
Formula	1.2-3
fs	1.3.1	1.5.0
futile.logger	1.4.3
futile.options	1.0.1
future	1.14.0
future.apply	1.3.0
gbRd	0.4-11
gdata	2.18.0
genefilter	1.72.1
geneLenDataBase	1.20.0
geneplotter	1.62.0
generics	0.0.2	0.1.0
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	3.3.2
ggrepel	0.8.1
ggridges	0.5.1
gh	1.1.0
gistr	0.4.2	0.9.0
git2r	0.27.1
Glimma	1.12.0
glmnet		4.0-2
globals	0.12.4
glue	1.4.1	1.4.2
gmodels	2.18.1
GO.db	3.4.1
GOplot	1.0.2

goseq	1.36.0
gower	0.2.1	0.2.2
gplots	3.0.1.1
graphics	4.0.3	4.0.3
grDevices	4.0.3	4.0.3
grid	4.0.3	4.0.3
gridExtra	2.3
gsubfn	0.7
gtable	0.3.0	0.3.0
gtools	3.8.1
haven	2.1.1	2.3.1
hdf5r	1.2.0
hexbin	1.27.3	1.28.1
highr	0.8	0.8
Hmisc	4.4-0
hms	0.5.0	0.5.3
htmlTable	1.13.1
htmltools	0.3.6	0.5.0
htmlwidgets	1.3	1.5.2
httpcode		0.3.0
httpuv	1.5.1	1.5.4
httr	1.4.1	1.4.2
hwriter	1.3.2
ica	1.0-2
igraph	1.2.4.1
ini	0.3.1
inline	0.3.15
ipred	0.9-9	0.9-9
IRanges	2.22.2
IRdisplay		0.7.0
IRkernel		1.1.1
irlba	2.3.3
isoband		0.2.2
iterators	1.0.12	1.0.13
janitor	1.2.0
jsonlite	1.6.1	1.7.1
kableExtra		1.3.1
KernSmooth	2.23-15	2.23-18
KernSmooth	2.23-18	2.23-18
knitr	1.28	1.30
labeling	0.3	0.4.2
lambda.r	1.2.3
later	0.8.0	1.1.0.1
lattice	0.20-38	0.20-41
lattice	0.20-41	0.20-41
latticeExtra	0.6-28
lava	1.6.6	1.6.8.1
lazyeval	0.2.2	0.2.2
leiden	0.3.1
lifecycle		0.2.0
limma	3.40.6
listenv	0.7.0
lme4	1.1-21
lmtest	0.9-37
locfit	1.5-9.1
loo	2.1.0
lsei	1.2-0
lubridate	1.7.4	1.7.9.2
magick	2.1
magrittr	1.5	2.0.1
maps	3.3.0	3.3.0
markdown	1.1	1.1
MASS	7.3-51.5	7.3-53
MASS	7.3-53.1	7.3-53
Matrix	1.2-17	1.2-18
Matrix	1.3-2	1.2-18
matrixStats	0.55.0
memoise	1.1.0
metap	1.1
methods	4.0.3	4.0.3
mgcv	1.8-28	1.8-33
mgcv	1.8-34	1.8-33
mime	0.7	0.9
minqa	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	3.1-141	3.1-150
nlme	3.1-152	3.1-150
nloptr	1.2.1
nnet	7.3-12	7.3-14
nnet	7.3-15	7.3-14
npsurv	0.4-0
numDeriv	2016.8-1.1	2016.8-1.1
openssl	1.4.1	1.4.3
openxlsx	4.1.0.1
pacman	0.5.1
parallel	4.0.3	4.0.3
parallelMap	1.4
ParamHelpers	1.12
pbapply	1.4-1
pbdZMQ		0.3-3.1
phangorn	2.5.5
phytools	0.6-99
pillar	1.4.2	1.4.7
pkgbuild	1.0.8	1.1.0
pkgconfig	2.0.2	2.0.3
pkgload	1.0.2	1.1.0
plogr	0.2.0
plotly	4.9.0	4.9.2.1
plotrix	3.7-6
plyr	1.8.4	1.8.6
png	0.1-7
praise	1.0.0	1.0.0
prettyunits	1.0.2	1.1.1
pROC		1.16.2
processx	3.4.1	3.4.4
prodlim	2018.04.18	2019.11.13
progress	1.2.2	1.2.2
promises	1.0.1	1.1.1
proto	1.0.0
pryr	0.1.4	0.1.4
ps	1.3.0	1.4.0
purrr	0.3.4	0.3.4
quadprog	1.5-7
quantmod	0.4-15	0.4.17
qvalue	2.16.0
R.methodsS3	1.7.1
R.oo	1.23.0
R.utils	2.9.0
R6	2.4.0	2.5.0
randomForest	4.6-14	4.6-14
RANN	2.6.1
rappdirs	0.3.1	0.3.1
rbokeh	0.5.0	0.5.1
rcmdcheck	1.3.3
RColorBrewer	1.1-2	1.1-2
Rcpp	1.0.4.6	1.0.5
RcppAnnoy	0.0.12
RcppArmadillo	0.9.600.4.0
RcppEigen	0.3.3.5.0
RcppParallel	4.4.3
RcppProgress	0.4.1
RCurl	1.98-1.2
Rdpack	0.11-0
readr	1.3.1	1.4.0
readxl	1.3.1	1.3.1
recipes	0.1.6	0.1.15
rematch	1.0.1	1.0.1
rematch2	2.1.2	2.1.2
remotes	2.1.1
repr		1.1.0
reprex	0.3.0	0.3.0
reshape2	1.4.3	1.4.4
reticulate	1.15	1.18
rex	1.1.2
rhdf5	2.28.1
Rhdf5lib	1.6.3
Rhtslib	1.18.1
rlang	0.4.6	0.4.8
rmarkdown	1.14	2.5
ROCR	1.0-7
ROTS	1.12.0
roxygen2	7.1.0
rpart	4.1-15	4.1-15
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
rstudioapi	0.11	0.13
rsvd	1.0.2
rtracklayer	1.44.4
Rtsne	0.15
rversions	2.0.1
rvest	0.3.4	0.3.6
S4Vectors	0.26.1
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		1.4.5
shiny	1.3.2	1.5.0
sitmo	2.0.1
sm	2.2-5.6
snakecase	0.11.0
snow	0.4-3
sourcetools	0.1.7	0.1.7
spatial		7.3-12
splines	4.0.3	4.0.3
splitstackshape	1.4.8
sqldf	0.4-11
SQUAREM	2017.10-1	2020.5
StanHeaders	2.18.1-10
statmod	1.4.32
stats	4.0.3	4.0.3
stats4	4.0.3	4.0.3
stringi	1.4.3	1.5.3
stringr	1.4.0	1.4.0
SummarizedExperiment	1.18.2
survival	3.1-12	3.2-7
survival	3.2-7	3.2-7
sys	3.2	3.4
tcltk	4.0.3	4.0.3
testthat	2.3.2	3.0.0
tibble	2.1.3	3.0.4
tidyr	0.8.3	1.1.2
tidyselect	0.2.5	1.1.0
tidyverse	1.2.1	1.3.0
timeDate	3043.102	3043.102
tinytex	0.15	0.27
tools	4.0.3	4.0.3
triebeard		0.3.0
tsne	0.1-3
TTR	0.23-4	0.24.2
tximport	1.12.3
tximportData	1.18.0
urltools		1.7.3
usethis	1.6.1
utf8	1.1.4	1.1.4
utils	4.0.3	4.0.3
uuid		0.1-4
uwot	0.1.3
vctrs	0.2.0	0.3.5
viridis	0.5.1
viridisLite	0.3.0	0.3.0
waldo		0.2.3
webshot		0.5.2
whisker	0.3-2	0.4
withr	2.2.0	2.3.0
xfun	0.8	0.19
XML	3.98-1.20
xml2	1.3.2	1.3.2
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	0.1.0
zip	2.0.3
zlibbioc	1.30.0
zoo	1.8-6	1.8-8

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"))