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R is a free software environment for statistical computing and graphics.
Version | module name | notes |
---|---|---|
4.0.3 | r/4.0.3 | optimized for avx, avx2 and avx512 |
4.0.3 | anaconda3/2020.07 + conda/r |
Seminar Slides
- Programming (A. Pacheco, J. Mack)
- Visualization (A. Pacheco, J. Mack)
Which versions of R are available?
There are four version of R available, 3.3.3, 3.4.2, 3.4.3 and 3.5.3. Of the two 3.5.3 version, one version labelled r-bio contains packages from Bioconductor for Bioinformatics research.
Usage
module load r-project/3.3.3
module load r-project/3.4.2
module load anaconda/python3
module load r-project/3.5.3
module load r-bio/3.5.3
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.
The r-project/3.x.y modules sets up a variable, R_LIBS, to install packages in your home directory. Make sure the R_LIBS directory exists
mkdir -p ${R_LIBS}
Start interactive R session and install package using the command
install.packages('packagename')
Alternatively, you can add install.packages('packagename') within your R script
If you get an error installing packages locally, then use the command
install.packages('packagename',lib=Sys.getenv("R_LIBS"))
Installed Packages
Package | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | r-bio |
---|---|---|---|---|---|
abind | 1.4-5 | 1.4-5 | 1.4-3 | ||
acepack | 1.4.1 | ||||
amap | 0.8-16 | ||||
annotate | 1.58.0 | ||||
AnnotationDbi | 1.42.1 | ||||
ape | 5.3 | ||||
argparse | 1.1.1 | ||||
askpass | 1.1 | 1.1 | 1.1 | ||
assertthat | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 |
backports | 1.1.2 | 1.1.1 | 1.1.2 | 1.1.3 | 1.1.1 |
base | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
base64enc | 0.1-3 | 0.1-3 | 0.1-3 | 0.1-3 | 0.1-3 |
BH | 1.65.0-1 | 1.65.0-1 | 1.65.0-1 | 1.69.0-1 | 1.69.0-1 |
BiasedUrn | 1.07 | ||||
bindr | 0.1 | 0.1 | 0.1 | 0.1.1 | |
bindrcpp | 0.2 | 0.2 | 0.2 | 0.2.2 | |
Biobase | 2.40.0 | ||||
BiocGenerics | 0.26.0 | ||||
BiocParallel | 1.14.2 | ||||
biomaRt | 2.36.1 | ||||
Biostrings | 2.48.0 | ||||
bit | 1.1-12 | ||||
bit64 | 0.9-7 | ||||
bitops | 1.0-6 | 1.0-6 | 1.0-6 | 1.0-6 | |
blob | 1.1.0 | ||||
boot | 1.3-18 | 1.3-20 | 1.3-20 | 1.3-20 | 1.3-20 |
broom | 0.4.3 | 0.4.3 | 0.4.3 | 0.5.1 | |
callr | 3.2.0 | 2.0.1 | 1.0.0 | 3.1.1 | 3.0.0 |
car | 2.1-6 | ||||
caret | 6.0-78 | ||||
caTools | 1.17.1.2 | 1.17.1 | 1.17.1 | 1.17.1 | |
cellranger | 1.1.0 | 1.1.0 | 1.1.0 | 1.1.0 | 1.1.0 |
checkmate | 1.8.4 | ||||
chron | 2.3-51 | ||||
class | 7.3-14 | 7.3-14 | 7.3-14 | 7.3-15 | 7.3-15 |
cli | 1.0.0 | 1.0.0 | 1.0.0 | 1.0.1 | 1.0.1 |
clipr | 0.4.0 | 0.5.0 | 0.4.0 | 0.5.0 | 0.4.0 |
clisymbols | 1.2.0 | 1.2.0 | 1.2.0 | ||
cluster | 2.0.5 | 2.0.6 | 2.0.6 | 2.0.7-1 | 2.0.7-1 |
codetools | 0.2-15 | 0.2-15 | 0.2-15 | 0.2-16 | 0.2-16 |
colorspace | 1.3-2 | 1.3-2 | 1.3-2 | 1.4-0 | 1.3-2 |
compiler | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
covr | 3.0.1 | ||||
crayon | 1.3.4 | 1.3.4 | 1.3.4 | 1.3.4 | 1.3.4 |
ctc | 1.54.0 | ||||
curl | 3.1 | 3.1 | 3.1 | 3.3 | 3.3 |
CVST | 0.2-1 | ||||
datasets | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
data.table | 1.10.4-3 | 1.11.8 | |||
DBI | 0.7 | 0.7 | 0.7 | 1.0.0 | 0.7 |
dbplyr | 1.2.0 | 1.2.0 | 1.1.0 | 1.3.0 | 1.2.2 |
ddalpha | 1.3.1 | ||||
debugme | 1.1.0 | 1.1.0 | |||
DelayedArray | 0.6.5 | ||||
DEoptimR | 1.0-8 | ||||
desc | 1.2.0 | 1.2.0 | 1.2.0 | ||
devtools | 2.0.1 | 2.0.1 | 1.12.0 | ||
dichromat | 2.0-0 | 2.0-0 | 2.0-0 | 2.0-0 | |
digest | 0.6.14 | 0.6.12 | 0.6.13 | 0.6.18 | 0.6.12 |
dimRed | 0.1.0 | ||||
dplyr | 0.7.4 | 0.7.4 | 0.7.4 | 0.8.0.1 | 0.7.7 |
DRR | 0.0.2 | ||||
dygraphs | 1.1.1.6 | 1.1.1.4 | |||
ellipsis | 0.1.0 | 0.1.0 | 0.1.0 | ||
evaluate | 0.10.1 | 0.10.1 | 0.10.1 | 0.13 | 0.10.1 |
fansi | 0.4.0 | 0.4.0 | 0.4.0 | 1.1.25 | |
fftwtools | 0.9-8 | ||||
findpython | 1.0.3 | ||||
flexdashboard | 0.5.1.1 | 0.5.1 | |||
forcats | 0.2.0 | 0.2.0 | 0.2.0 | 0.4.0 | 0.2.0 |
foreach | 1.4.4 | ||||
foreign | 0.8-67 | 0.8-69 | 0.8-69 | 0.8-71 | 0.8-71 |
formatR | 1.5 | ||||
fs | 1.2.6 | 1.2.7 | 1.2.6 | ||
genefilter | 1.62.0 | ||||
GenomeInfoDb | 1.16.0 | ||||
GenomeInfoDbData | 1.1.0 | ||||
GenomicRanges | 1.32.6 | ||||
generics | 0.0.2 | 0.0.2 | 0.0.2 | ||
ggplot2 | 2.2.1 | 2.2.1 | 2.2.1 | 3.1.0 | 3.2.0 |
gh | 1.0.1 | 1.0.1 | 1.0.1 | ||
git2r | 0.24.0 | 0.25.2 | 0.24.0 | 0.18.0 | |
glmnet | 2.0-13 | ||||
glue | 1.2.0 | 1.2.0 | 1.2.0 | 1.3.1 | 1.2.0 |
gower | 0.1.2 | ||||
graphics | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
grDevices | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
grid | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
gtable | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 |
gtools | 3.8.1 | 3.5.0 | 3.5.0 | ||
haven | 1.1.1 | 1.1.1 | 1.1.0 | 2.1.0 | 1.1.0 |
hexbin | 1.27.1 | ||||
highr | 0.6 | 0.6 | 0.6 | 0.7 | 0.6 |
hms | 0.4.0 | 0.4.1 | 0.4.0 | 0.4.2 | 0.3 |
htmltools | 0.3.6 | 0.3.6 | 0.3.6 | 0.3.6 | 0.3.6 |
htmlwidgets | 1.3 | 0.9 | 0.9 | 0.9 | |
httpuv | 1.5.1 | 1.3.5 | 1.3.5 | 1.3.5 | |
httr | 1.3.1 | 1.3.1 | 1.3.1 | 1.4.0 | 1.3.1 |
ini | 0.3.1 | 0.3.1 | 0.3.1 | ||
ipred | 0.9-6 | ||||
IRdisplay | 0.4.4 | ||||
IRkernel | 0.8.11 | ||||
iterators | 1.0.9 | ||||
jsonlite | 1.5 | 1.5 | 1.5 | 1.6 | 1.5 |
kernlab | 0.9-25 | ||||
KernSmooth | 2.23-15 | 2.23-15 | 2.23-15 | 2.23-15 | 2.23-15 |
knitr | 1.18 | 1.19 | 1.18 | 1.22 | |
labeling | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 |
later | 0.8.0 | ||||
lattice | 0.20-34 | 0.20-35 | 0.20-35 | 0.20-38 | 0.20-38 |
lava | 1.5.1 | ||||
lazyeval | 0.2.1 | 0.2.0 | 0.2.1 | 0.2.1 | 0.2.0 |
lme4 | 1.1-15 | ||||
lubridate | 1.7.1 | 1.7.2 | 1.7.1 | 1.7.4 | 1.7.1 |
magrittr | 1.5 | 1.5 | 1.5 | 1.5 | 1.5 |
maps | 3.2.0 | ||||
markdown | 0.8 | 0.8 | 0.8 | 0.9 | 0.8 |
MASS | 7.3-45 | 7.3-47 | 7.3-48 | 7.3-51.1 | 7.3-51.1 |
Matrix | 1.2-8 | 1.2-11 | 1.2-12 | 1.2-15 | 1.2-15 |
MatrixModels | 0.4-1 | 0.52.2 | |||
matrixStats | 0.54.0 | 0.53.1 | |||
memoise | 1.1.0 | 1.1.0 | 1.1.0 | 1.1.0 | |
methods | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
mgcv | 1.8-17 | 1.8-20 | 1.8-22 | 1.8-27 | 1.8-27 |
mime | 0.5 | 0.5 | 0.5 | 0.6 | 0.5 |
minqa | 1.2.4 | ||||
mnormt | 1.5-5 | 1.5-5 | 1.5-5 | 1.5-5 | |
ModelMetrics | 1.1.0 | ||||
modelr | 0.1.1 | 0.1.1 | 0.1.1 | 0.1.4 | |
munsell | 0.4.3 | 0.4.3 | 0.4.3 | 0.5.0 | 0.4.3 |
nlme | 3.1-131 | 3.1-131 | 3.1-131 | 3.1-137 | 3.1-137 |
nloptr | 1.0.4 | ||||
nnet | 7.3-12 | 7.3-12 | 7.3-12 | 7.3-12 | 7.3-12 |
numDeriv | 2016.8-1 | ||||
openssl | 0.9.9 | 0.9.9 | 0.9.9 | 1.2.2 | 0.9.7 |
optparse | 1.6.0 | ||||
padr | 0.4.1 | 0.4.0 | |||
parallel | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
pbdZMQ | 0.3-0 | ||||
pbkrtest | 0.4-7 | ||||
phangorn | 2.5.5 | ||||
pillar | 1.1.0 | 1.1.0 | 1.0.1 | 1.3.1 | 1.3.1 |
pkgbuild | 1.0.2 | 1.0.3 | 1.0.2 | ||
pkgconfig | 2.0.1 | 2.0.1 | 2.0.1 | 2.0.2 | 2.0.2 |
pkgload | 1.0.2 | 1.0.2 | 1.0.2 | ||
plogr | 0.1-1 | 0.1-1 | 0.1-1 | 0.2.0 | 0.2.0 |
plot3D | 1.1.1 | ||||
plyr | 1.8.4 | 1.8.4 | 1.8.4 | 1.8.4 | 1.8.4 |
png | 0.1-7 | 0.1-7 | |||
pracma | 2.2.5 | 2.1.4 | |||
praise | 1.0.0 | 1.0.0 | 1.0.0 | ||
prettyunits | 1.0.2 | 1.0.2 | 1.0.2 | 1.0.2 | |
processx | 3.3.0 | 3.3.0 | 3.3.0 | 3.2.0 | |
prodlim | 1.6.1 | ||||
progress | 1.2.0 | 1.2.0 | 1.2.0 | 1.1.2 | |
promises | 1.0.1 | ||||
proto | 1.0.0 | 1.0.0 | |||
ps | 1.3.0 | 1.3.0 | 1.3.0 | 1.1.0 | |
psych | 1.7.8 | 1.7.8 | 1.7.8 | ||
purrr | 0.2.4 | 0.2.4 | 0.2.4 | 0.3.1 | 0.2.4 |
quantmod | 0.4-12 | ||||
quantreg | 5.34 | ||||
R6 | 2.2.2 | 2.2.2 | 2.2.2 | 2.4.0 | 2.2.2 |
randomForest | 4.6-12 | ||||
rbokeh | 0.6.3 | ||||
rcmdcheck | 1.3.2 | 1.3.2 | 1.3.2 | ||
RColorBrewer | 1.1-2 | 1.1-2 | 1.1-2 | 1.1-2 | |
Rcpp | 0.12.15 | 0.12.13 | 0.12.14 | 1.0.0 | 1.0.0 |
RcppArmadillo | 0.8.100.1.0 | ||||
RcppEigen | 0.3.3.3.1 | ||||
RcppRoll | 0.2.2 | ||||
RCurl | 1.95-4.8 | ||||
readr | 1.1.1 | 1.1.1 | 1.1.1 | 1.3.1 | 1.1.1 |
readxl | 1.0.0 | 1.0.0 | 1.0.0 | 1.3.1 | 1.1.0 |
recipes | 0.1.1 | ||||
rematch | 1.0.1 | 1.0.1 | 1.0.1 | 1.0.1 | 1.0.1 |
remotes | 2.0.2 | 2.0.4 | 2.0.2 | ||
repr | 0.12.0 | ||||
reprex | 0.1.1 | 0.1.2 | 0.1.1 | 0.2.1 | |
reshape2 | 1.4.3 | 1.4.2 | 1.4.3 | 1.4.3 | 1.4.2 |
RJSONIO | 1.3-0 | ||||
rlang | 0.1.6 | 0.1.6 | 0.1.6 | 0.3.1 | 0.3.1 |
rmarkdown | 1.8 | 1.6 | 1.8 | 1.12 | |
R.matlab | 3.6.2 | 3.6.1 | |||
R.methodsS3 | 1.7.1 | 1.7.1 | |||
Rmpi | 0.6-6 | ||||
robustbase | 0.92-8 | ||||
R.oo | 1.22.0 | 1.21.0 | |||
rpart | 4.1-10 | 4.1-11 | 4.1-11 | 4.1-13 | 4.1-13 |
rprojroot | 1.3-2 | 1.2 | 1.3-1 | 1.3-2 | 1.2 |
Rsamtools | 1.32.2 | ||||
RSQLite | 2.0 | ||||
rstudioapi | 0.7 | 0.7 | 0.7 | 0.9.0 | 0.7 |
R.utils | 2.8.0 | 2.5.0 | |||
rvest | 0.3.2 | 0.3.2 | 0.3.2 | 0.3.2 | 0.3.2 |
rzmq | 0.9.3 | ||||
S4Vectors | 0.18.3 | ||||
scales | 0.5.0 | 0.5.0 | 0.5.0 | 1.0.0 | 0.5.0 |
selectr | 0.3-1 | 0.3-1 | 0.3-1 | 0.4-1 | 0.3-1 |
sessioninfo | 1.1.1 | 1.1.1 | 1.1.1 | ||
sfsmisc | 1.1-1 | ||||
shiny | 1.3.0 | 1.0.5 | 1.0.5 | 1.0.5 | |
snow | 0.4-2 | ||||
sourcetools | 0.1.7 | 0.1.6 | 0.1.6 | 0.1.6 | |
SparseM | 1.77 | ||||
spatial | 7.3-11 | 7.3-11 | 7.3-11 | 7.3-11 | 7.3-11 |
splines | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
stats | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
stats4 | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
stringi | 1.1.6 | 1.1.5 | 1.1.6 | 1.4.3 | 1.1.5 |
stringr | 1.2.0 | 1.2.0 | 1.2.0 | 1.4.0 | 1.2.0 |
survival | 2.40-1 | 2.41-3 | 2.41-3 | 2.43-3 | 2.43-3 |
sys | 3.1 | 3.1 | 3.1 | ||
tcltk | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
testthat | 2.0.1 | 2.0.0 | 1.0.2 | ||
tibble | 1.4.1 | 1.4.2 | 1.4.1 | 2.0.1 | 2.0.1 |
tidyr | 0.7.2 | 0.8.0 | 0.7.2 | 0.8.3 | 0.7.2 |
tidyselect | 0.2.3 | 0.2.3 | 0.2.3 | 0.2.5 | 0.2.3 |
tidyverse | 1.2.1 | 1.2.1 | 1.2.1 | 1.2.1 | |
timeDate | 3042.101 | ||||
tinytex | 0.11 | 0.11 | 0.11 | ||
tools | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
TTR | 0.23-2 | ||||
usethis | 1.4.0 | 1.4.0 | |||
utf8 | 1.1.3 | 1.1.3 | 1.1.2 | 1.1.4 | 1.1.3 |
utils | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 |
uuid | 0.1-2 | ||||
viridisLite | 0.2.0 | 0.2.0 | 0.2.0 | 0.3.0 | 0.2.0 |
whisker | 0.3-2 | 0.3-2 | 0.3-2 | 0.3-2 | 0.3-2 |
withr | 2.1.2 | 2.1.2 | 2.1.1 | 2.1.2 | 2.1.2 |
xfun | 0.6 | 0.6 | 0.5 | ||
XML | 3.98-1.9 | ||||
xml2 | 1.1.1 | 1.2.0 | 1.1.1 | 1.2.0 | 1.1.1 |
xopen | 1.0.0 | 1.0.0 | 1.0.0 | ||
xtable | 1.8-3 | 1.8-2 | 1.8-2 | 1.8-2 | |
xts | 0.11-2 | 0.10-1 | 0.10-1 | ||
XVector | 0.20.0 | ||||
yaml | 2.1.16 | 2.1.14 | 2.1.16 | 2.2.0 | 2.1.14 |
zlibbioc | 1.26.0 | ||||
zoo | 1.8-5 | 1.8-0 | 1.8-0 |
Installed Packages
Coming Soon
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"))
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