R v3.5.0

R is a software environment for statistical computing and graphics.

Accessing the software

To load the module:

$ module load R/3.5.0-iomkl-2018a-X11-20180131

An example command to include in your job script:

$ R -f <R-script>

Example: R Job

An example can be found at ${BB_EXAMPLES}/R/3.5.0/sbatch.sh. The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/R/3.5.0 ~/r-3.5.0-test
$ cd ~/r-3.5.0-test

Edit the sbatch.sh script according to your needs, then do:

$ sbatch sbatch.sh

Additional Packages

We recommend that you do not install R packages into a local, user library. Due to the heterogeneous nature of BlueBEAR, this often causes conflicts and crashes.

List of currently installed packages

Package

Version
abc 2.1
abc.data 1.0
abind 1.4-5
acepack 1.4.1
adabag 4.2
ade4 1.7-10
adegenet 2.1.1
adephylo 1.1-11
ADGofTest 0.3
akima 0.6-2
AlgDesign 1.1-7.3
animation 2.5
aod 1.3
ape 5.0
arm 1.9-3
assertthat 0.2.0
AUC 0.3.0
audio 0.1-5
backports 1.1.2
base64 2.0
base64enc 0.1-3
BatchJobs 1.7
BayesianTools 0.1.4
BB 2014.10-1
BBmisc 1.11
BDgraph 2.44
beanplot 1.2
beeswarm 0.2.3
BH 1.66.0-1
BiasedUrn 1.07
bigmemory 4.5.33
bigmemory.sri 0.1.3
bindr 0.1.1
bindrcpp 0.2
bio3d 2.3-3
biom 0.3.12
bit 1.1-12
bit64 0.9-7
bitops 1.0-6
blob 1.1.0
bmp 0.3
bnlearn 4.3
bold 0.5.0
boot 1.3-20
bootstrap 2017.2
brew 1.0-6
brglm 0.6.1
bridgesampling 0.4-0
Brobdingnag 1.2-4
broom 0.4.3
bst 0.3-14
Cairo 1.5-9
calibrate 1.7.2
callr 2.0.2
car 2.1-6
caret 6.0-78
caTools 1.17.1
cellranger 1.1.0
cgdsr 1.2.10
cghFLasso 0.2-1
checkmate 1.8.5
chemometrics 1.4.2
chron 2.3-52
circlize 0.4.3
class 7.3-14
classInt 0.1-24
cli 1.0.0
clipr 0.4.0
cluster 2.0.6
clusterGeneration 1.3.4
clusterRepro 0.5-1.1
clValid 0.6-6
coda 0.19-1
codetools 0.2-15
coin 1.2-2
colorspace 1.3-2
combinat 0.0-8
commonmark 1.4
corpcor 1.6.9
cowplot 0.9.2
crayon 1.3.4
crosstalk 1.0.0
crul 0.5.2
cubature 1.3-11
curl 3.1
cvAUC 1.1.0
CVST 0.2-1
d3Network 0.5.2.1
data.table 1.10.4-3
DBI 0.8
dbplyr 1.2.1
ddalpha 1.3.1.1
deal 1.2-37
debugme 1.1.0
deldir 0.1-14
dendextend 1.7.0
DEoptimR 1.0-8
Deriv 3.8.4
desc 1.1.1
deSolve 1.20
devtools 1.13.5
DHARMa 0.1.5
diagram 1.6.4
DiagrammeR 1.0.0
dichromat 2.0-0
digest 0.6.15
dimRed 0.1.0
diptest 0.75-7
DiscriMiner 0.1-29
dismo 1.1-4
distillery 1.0-4
DistributionUtils 0.5-1
diveRsity 1.9.90
doMC 1.3.5
doParallel 1.0.11
doRNG 1.6.6
doSNOW 1.0.16
dotCall64 0.9-5.2
downloader 0.4
dplyr 0.7.4
DRR 0.0.3
DT 0.4
dummies 1.5.6
dynamicTreeCut 1.63-1
e1071 1.6-8
EasyABC 1.5
ellipse 0.4.1
emulator 1.2-15
evaluate 0.10.1
expm 0.999-2
expsmooth 2.3
extrafont 0.17
extrafontdb 1.0
extRemes 2.0-8
FactoMineR 1.39
fail 1.3
fastcluster 1.1.24
fastICA 1.2-1
fastmatch 1.1-0
fdrtool 1.2.15
fdrtool 1.2.15
feather 0.3.1
ff 2.2-13
ffbase 0.12.3
fftw 1.0-4
fields 9.6
filehash 2.4-1
flashClust 1.01-2
flexclust 1.3-5
flexmix 2.3-14
fma 2.3
FME 1.3.5
FNN 1.1
forcats 0.3.0
foreach 1.4.4
forecast 8.2
foreign 0.8-69
formatR 1.5
Formula 1.2-2
fossil 0.3.7
fpc 2.1-11
fpp 0.5
fracdiff 1.4-2
futile.logger 1.4.3
futile.options 1.0.0
future 1.7.0
gam 1.15
gamlss.data 5.0-0
gamlss.dist 5.0-4
gap 1.1-21
gapfill 0.9.6
gbm 2.1.3
gclus 1.3.1
gdalUtils 2.0.1.7
gdata 2.18.0
gdistance 1.2-1
geepack 1.2-1
geiger 2.0.6
GeneNet 1.2.13
geometry 0.3-6
getopt 1.20.2
GetoptLong 0.1.6
GGally 1.3.2
ggbeeswarm 0.6.0
ggm 2.3
ggplot2 2.2.1
ggvis 0.4.3
git2r 0.21.0
glasso 1.8
glmmML 1.0.2
glmnet 2.0-13
GlobalOptions 0.0.12
globals 0.11.0
glue 1.2.0
gmm 1.6-1
gmodels 2.16.2
goftest 1.1-1
gomms 1.0
gower 0.1.2
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.3
GSA 1.03
gsalib 2.1
gsw 1.0-5
gtable 0.2.0
gtools 3.5.0
haven 1.1.1
heatmap3 1.1.1
hexbin 1.27.2
highr 0.6
Hmisc 4.1-1
hms 0.4.2
htmlTable 1.11.2
htmltools 0.3.6
htmlwidgets 1.0
httpcode 0.2.0
httpuv 1.3.6.2
httr 1.3.1
huge 1.2.7
hwriter 1.3.2
HWxtest 1.1.7
IDPmisc 1.1.17
igraph 1.2.1
imager 0.40.2
ineq 0.2-13
influenceR 0.1.0
infotheo 1.2.0
interpretR 0.2.4
ipred 0.9-6
irace 2.4
irlba 2.3.2
Iso 0.0-17
iterators 1.0.9
JBTools 0.7.2.9
jpeg 0.1-8
jsonlite 1.5
kernlab 0.9-25
KernSmooth 2.23-15
klaR 0.6-13
knitr 1.20
kohonen 3.0.4
ks 1.11.0
labdsv 1.8-0
labeling 0.3
labelled 1.0.1
laeken 0.4.6
lambda.r 1.2
lars 1.2
lattice 0.20-35
latticeExtra 0.6-28
lava 1.6
lavaan 0.5-23.1097
lazy 1.2-15
lazyeval 0.2.1
leaps 3.0
LearnBayes 2.15
lhs 0.16
limSolve 1.5.5.3
listenv 0.7.0
lme4 1.1-15
Lmoments 1.2-3
lmtest 0.9-35
locfit 1.5-9.1
logcondens 2.1.5
logistf 1.22
logspline 2.1.9
longitudinal 1.1.12
longmemo 1.0-0
lpSolve 5.6.13
lubridate 1.7.3
magic 1.5-8
magrittr 1.5
maps 3.2.0
maptools 0.9-2
markdown 0.8
MASS 7.3-49
Matrix 1.2-12
matrixcalc 1.0-3
MatrixModels 0.4-1
matrixStats 0.53.1
maxLik 1.3-4
mboost 2.8-1
mclust 5.4
mediation 4.4.6
memoise 1.1.0
memuse 4.0-0
mgcv 1.8-23
mi 1.0
mice 2.46.0
mime 0.5
miniUI 0.1.1
minpack.lm 1.2-1
minqa 1.2.4
misc3d 0.8-4
miscTools 0.6-22
mixtools 1.1.0
mlbench 2.1-1
mlogit 0.2-4
mlr 2.12
mnormt 1.5-5
ModelMetrics 1.1.0
modelr 0.1.1
modeltools 0.2-21
moments 0.14
mpath 0.3-4
msm 1.6.6
multcomp 1.4-8
multicool 0.1-10
munsell 0.4.3
mvtnorm 1.0-7
natserv 0.1.4
ncbit 2013.03.29
network 1.13.0
neuRosim 0.2-12
nleqslv 3.3.1
nlme 3.1-131.1
nloptr 1.0.4
NLP 0.1-11
NMF 0.21.0
nnet 7.3-12
nnls 1.4
nor1mix 1.2-3
np 0.60-6
numDeriv 2016.8-1
oce 0.9-23
OceanView 1.0.4
openssl 1.0.1
openxlsx 4.0.17
optparse 1.4.4
ordinal 2015.6-28
parallelMap 1.3
ParamHelpers 1.10
party 1.2-4
pastecs 1.3-18
pbapply 1.3-4
pbivnorm 0.6.0
pbkrtest 0.4-7
pcaPP 1.9-73
penalized 0.9-50
peperr 1.1-7
permute 0.9-4
phangorn 2.4.0
pheatmap 1.0.8
phylobase 0.8.4
pillar 1.2.1
pim 2.0.1
pinfsc50 1.1.0
pixmap 0.4-11
pkgconfig 2.0.1
pkgmaker 0.22
plogr 0.2.0
plot3D 1.1.1
plot3Drgl 1.0.1
plotrix 3.7
pls 2.6-0
plyr 1.8.4
png 0.1-7
PoissonSeq 1.1.2
polspline 1.1.12
polyclip 1.6-1
polynom 1.3-9
prabclus 2.2-6
pracma 2.1.4
praise 1.0.0
prettyunits 1.0.2
pROC 1.10.0
prodlim 1.6.1
profileModel 0.5-9
progress 1.1.2
proto 1.0.0
proxy 0.4-21
pryr 0.1.4
pscl 1.5.2
pspline 1.0-18
psych 1.7.8
purrr 0.2.4
pvclust 2.0-0
qgraph 1.4.4
qrnn 2.0.2
quadprog 1.5-5
quantmod 0.4-12
quantreg 5.35
questionr 0.6.2
R.cache 0.13.0
R.matlab 3.6.1
R.methodsS3 1.7.1
R.oo 1.21.0
R.rsp 0.42.0
R.utils 2.6.0
R6 2.2.2
randomForest 4.6-12
randomForestSRC 2.5.1
ranger 0.9.0
RANN 2.5.1
raster 2.6-7
RCircos 1.2.0
RColorBrewer 1.1-2
Rcpp 0.12.16
RcppArmadillo 0.8.400.0.0
RcppEigen 0.3.3.4.0
RcppProgress 0.4
RcppRoll 0.2.2
RCurl 1.95-4.10
readbitmap 0.1-4
readr 1.1.1
readxl 1.0.0
recipes 0.1.2
registry 0.5
rematch 1.0.1
rentrez 1.2.1
reprex 0.1.2
reshape 0.8.7
reshape2 1.4.3
RGCCA 2.1.2
rgdal 1.2-16
rgexf 0.15.3
rgl 0.99.9
RInside 0.2.14
ritis 0.7.0
rJava 0.9-9
rjson 0.2.15
RJSONIO 1.3-0
rlang 0.2.0
rlecuyer 0.3-4
rmarkdown 1.9
rmeta 2.16
Rmpi 0.6-6
rms 5.1-2
RMTstat 0.3
rncl 0.8.2
RNeXML 2.0.8
rngtools 1.2.4
robustbase 0.92-8
ROCR 1.0-7
Rook 1.1-1
rootSolve 1.7
rotl 3.0.3
roxygen2 6.0.1
rpart 4.1-13
rprojroot 1.3-2
rrcov 1.4-3
rredlist 0.4.0
RSNNS 0.4-10
RSQLite 2.0
Rssa 1.0
rstudioapi 0.7
Rtsne 0.13
Rttf2pt1 1.3.6
RUnit 0.4.31
rversions 1.0.3
rvest 0.3.2
RWeka 0.4-37
RWekajars 3.9.2-1
sandwich 2.4-0
scales 0.5.0
scatterplot3d 0.3-41
seewave 2.1.0
segmented 0.5-3.0
selectr 0.3-2
sem 3.1-9
sendmailR 1.2-1
seqinr 3.4-5
sfsmisc 1.1-2
shape 1.4.4
shapefiles 0.7
shiny 1.0.5
shinydashboard 0.6.1
signal 0.7-6
SimSeq 1.4.0
slam 0.1-42
sm 2.2-5.4
smoother 1.1
sn 1.5-1
sna 2.4
snow 0.4-2
snowfall 1.84-6.1
solrium 1.0.0
som 0.3-5.1
soundecology 1.3.3
sourcetools 0.1.6
sp 1.2-7
spam 2.1-2
SparseM 1.77
spatial 7.3-11
spatstat 1.55-0
spatstat.data 1.2-0
spatstat.utils 1.8-0
spData 0.2.8.1
spdep 0.7-4
SQUAREM 2017.10-1
stabledist 0.7-1
stabs 0.6-3
statmod 1.4.30
statnet.common 4.0.0
stringi 1.1.7
stringr 1.3.0
strucchange 1.5-1
subplex 1.5-2
SuperLearner 2.0-23
SuppDists 1.1-9.4
survival 2.41-3
survivalROC 1.0.3
svd 0.4.1
taxize 0.9.2
tclust 1.3-1
TeachingDemos 2.10
tensor 1.5
tensorA 0.36
testthat 2.0.0
TH.data 1.0-8
tibble 1.4.2
tidyr 0.8.0
tidyselect 0.2.4
tidyverse 1.2.1
timeDate 3043.102
timereg 1.9.2
tkrplot 0.0-23
tm 0.7-3
tmvtnorm 1.4-10
TraMineR 2.0-8
tree 1.0-38
triebeard 0.3.0
trimcluster 0.1-2
tripack 1.3-8
tseries 0.10-43
tseriesChaos 0.1-13
tsne 0.1-3
TTR 0.23-3
tuneR 1.3.2
ucminf 1.1-4
unbalanced 2.0
uniqueAtomMat 0.1-3-2
urca 1.3-0
urltools 1.7.0
utf8 1.1.3
uuid 0.1-2
vcd 1.4-4
vcfR 1.7.0
vegan 2.4-6
VennDiagram 1.6.19
VGAM 1.0-5
VIM 4.7.0
vioplot 0.2
vipor 0.4.5
viridis 0.5.0
viridisLite 0.3.0
visNetwork 2.0.3
waveslim 1.7.5
whisker 0.3-2
WikidataR 1.4.0
WikipediR 1.5.0
wikitaxa 0.2.0
withr 2.1.1
worrms 0.2.0
WriteXLS 4.0.0
xlsx 0.5.7
xlsxjars 0.6.1
XML 3.98-1.10
xml2 1.2.0
xtable 1.8-2
xts 0.10-2
yaml 2.1.18
zoo 1.8-1

An extensive list of currently installed packages can be viewed by issuing the following command from the R interpreter with the module loaded:

$ library()

Further R libraries are available. See Extra R Libraries for details.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations

None.

Other Information

The Support Level  for this application is An.

See the R project website for more information about this application.


Last modified: 5 July 2019