#

R

NOTE: This documentation assumes use of the new lmod module system on the cluster. See this page for details. In particular you need to activate the lmod system with the following command: source new-modules.sh or add it to your .bashrc so that it loads every time you log in (new accounts will have this in the .bashrc already).

When loading R from the Lmod system, 100s of common packages have already been installed. The list is available here. However, if you need to install new packages locally, you don't need to do much more than set an environment variable.

Use the R_LIBS_USER environment variable to specify local R package installations

The R_LIBS_USER environment variable is used by R to determine where packages should be installed when the install.packages() function is called. Simply specify your preferred path by setting this variable in your .bashrc.

module load R
...
export R_LIBS_USER=$HOME/apps/R:$R_LIBS_USER

Note that your change to the R_LIBS_USER variable should occur after R is loaded. This ensures that your local library is the first one checked by R for installs and libraries. Now when you use the install.packages() function, the package will be installed in the specified directory.

Local installation of an R package using the R_LIBS_USER environment variable

Packages in R

> installed.packages()
...
Version Priority
ADGofTest "0.3" NA
AnDE "1.0" NA
BB "2014.1-1" NA
Brobdingnag "1.2-4" NA
CpGassoc "2.11" NA
DBI "0.2-7" NA
DEoptimR "1.0-1" NA
Defaults "1.1-1" NA
FNN "1.1" NA
Formula "1.1-1" NA
GSA "1.03" NA
GWAF "2.1" NA
GenABEL "1.8-0" NA
GenABEL.data "1.0.0" NA
Hmisc "3.14-4" NA
MCMCpack "1.3-3" NA
MatchIt "2.4-21" NA
MetaSKAT "0.40" NA
NLP "0.1-3" NA
R.methodsS3 "1.6.1" NA
R2WinBUGS "2.1-19" NA
RColorBrewer "1.0-5" NA
RCurl "1.95-4.1" NA
RJSONIO "1.2-0.2" NA
RSQLite "0.11.4" NA
RSQLite.extfuns "0.0.1" NA
RSiena "1.1-232" NA
Rcmdr "2.0-4" NA
Rcpp "0.11.2" NA
RcppArmadillo "0.4.300.8.0" NA
RcppEigen "0.3.2.1.2" NA
Rserve "1.7-3" NA
SKAT "0.95" NA
SnowballC "0.5" NA
SparseM "1.03" NA
TH.data "1.0-3" NA
TTR "0.22-0" NA
XML "3.98-1.1" NA
abind "1.4-0" NA
akima "0.5-11" NA
amap "0.8-12" NA
aod "1.3" NA
ape "3.1-2" NA
aplpack "1.2.9" NA
arm "1.7-03" NA
base64 "1.1" NA
bdsmatrix "1.3-1" NA
beanplot "1.1" NA
bitops "1.0-6" NA
caTools "1.17" NA
car "2.0-20" NA
chron "2.3-45" NA
coda "0.16-1" NA
colorspace "1.2-4" NA
corpcor "1.6.6" NA
coxme "2.2-3" "optional"
cubature "1.1-2" NA
data.table "1.9.2" NA
deSolve "1.10-9" NA
devtools "1.5" NA
dichromat "2.0-0" NA
digest "0.6.4" NA
discretization "1.0-1" NA
doParallel "1.0.8" NA
doRNG "1.6" NA
doSNOW "1.0.12" NA
dynamicTreeCut "1.62" NA
e1071 "1.6-3" NA
effects "3.0-0" NA
evaluate "0.5.5" NA
expm "0.99-1.1" NA
fBasics "3010.86" NA
fastICA "1.2-0" NA
fastcluster "1.1.13" NA
fastmatch "1.0-4" NA
fields "7.1" NA
flashClust "1.01-2" NA
foreach "1.4.2" NA
forecast "5.4" NA
formatR "0.10" NA
formula.tools "1.3.4" NA
fracdiff "1.4-2" NA
functional "0.4" NA
gdata "2.13.3" NA
geepack "1.1-6" NA
ggplot2 "1.0.0" NA
glmnet "1.9-8" NA
gplots "2.14.1" NA
gridExtra "0.9.1" NA
grplasso "0.4-3" NA
gss "2.1-2" NA
gsubfn "0.6-5" NA
gtable "0.1.2" NA
gtools "3.4.1" NA
highr "0.3" NA
httr "0.3" NA
hwriter "1.3" NA
igraph "0.7.1" NA
inline "0.3.13" NA
intervals "0.14.0" NA
iterators "1.0.7" NA
itertools "0.1-3" NA
kernlab "0.9-19" NA
knitr "1.6" NA
labeling "0.2" NA
lasso2 "1.2-19" NA
latticeExtra "0.6-26" NA
lda "1.3.2" NA
leaps "2.9" NA
lhs "0.10" NA
lme4 "1.1-6" NA
lmtest "0.9-33" NA
locfit "1.5-9.1" NA
maps "2.3-7" NA
maptools "0.8-30" NA
markdown "0.7" NA
matrixStats "0.10.0" NA
matrixcalc "1.0-3" NA
mclust "4.3" NA
memoise "0.2.1" NA
meta "3.6-0" NA
mi "0.09-18.03" NA
mime "0.1.1" NA
minqa "1.2.3" NA
mlbench "2.1-1" NA
mlegp "3.1.4" NA
modeltools "0.2-21" NA
msm "1.3" NA
multcomp "1.3-3" NA
multicore "0.2" NA
munsell "0.4.2" NA
mvtnorm "0.9-99992" NA
nleqslv "2.2" NA
nor1mix "1.1-4" NA
numDeriv "2012.9-1" NA
operator.tools "1.3.0" NA
optmatch "0.9-1" NA
pROC "1.7.3" NA
penalized "0.9-42" NA
penalizedSVM "1.1" NA
permute "0.8-3" NA
phangorn "1.99-7" NA
pkgmaker "0.22" NA
plotrix "3.5-7" NA
plyr "1.8.1" NA
proto "0.3-10" NA
pspline "1.0-16" NA
psych "1.4.5" NA
quadprog "1.5-5" NA
quantmod "0.4-0" NA
quantreg "5.05" NA
randomForest "4.6-7" NA
raster "2.2-31" NA
registry "0.2" NA
relimp "1.0-3" NA
reshape "0.8.5" NA
reshape2 "1.4" NA
rgl "0.93.996" NA
rngtools "1.2.4" NA
robustbase "0.91-1" NA
rootSolve "1.6.5" NA
sandwich "2.3-0" NA
sas7bdat "0.5" NA
scales "0.2.4" NA
scatterplot3d "0.3-35" NA
sem "3.1-4" NA
slam "0.1-32" NA
snow "0.3-13" NA
sp "1.0-15" NA
spam "0.41-0" NA
sqldf "0.4-7.1" NA
stabledist "0.6-6" NA
statmod "1.4.20" NA
stringr "0.6.2" NA
strucchange "1.5-0" NA
subplex "1.1-4" NA
svmpath "0.953" NA
tcltk2 "1.2-10" NA
texreg "1.32" NA
tgp "2.4-9" NA
timeDate "3010.98" NA
timeSeries "3010.97" NA
tm "0.6" NA
tree "1.0-35" NA
truncnorm "1.0-7" NA
tseries "0.10-32" NA
vcd "1.3-1" NA
vegan "2.0-10" NA
whisker "0.3-2" NA
xtable "1.7-3" NA
xts "0.9-7" NA
zoo "1.7-11" NA
KernSmooth "2.23-12" "recommended"
MASS "7.3-31" "recommended"
Matrix "1.1-3" "recommended"
base "3.1.0" "base"
boot "1.3-11" "recommended"
class "7.3-10" "recommended"
cluster "1.15.2" "recommended"
codetools "0.2-8" "recommended"
compiler "3.1.0" "base"
datasets "3.1.0" "base"
foreign "0.8-61" "recommended"
grDevices "3.1.0" "base"
graphics "3.1.0" "base"
grid "3.1.0" "base"
lattice "0.20-29" "recommended"
methods "3.1.0" "base"
mgcv "1.7-29" "recommended"
nlme "3.1-117" "recommended"
nnet "7.3-8" "recommended"
parallel "3.1.0" "base"
rpart "4.1-8" "recommended"
spatial "7.3-8" "recommended"
splines "3.1.0" "base"
stats "3.1.0" "base"
stats4 "3.1.0" "base"
survival "2.37-7" "recommended"
tcltk "3.1.0" "base"
tools "3.1.0" "base"
utils "3.1.0" "base"

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