Page Comparison

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

...

Programming (A. Pacheco, J. Mack)
Visualization (A. Pacheco, J. Mack)

Installed Packages

R packages are built using SPACK optimized for the underlying CPU architecture or binary installs using Conda.

If you get an error installing packages locally, then use the command

Expand

Code Block

language	bash

install.packages('packagename',lib=Sys.getenv("R_LIBS"))

Installed Packages

Package

3.3.3

3.4.2

title	Deprecated CentOS 7.x Software: Use module load cent7 to use the following modules

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

Code Block

language	bash
title	R 3.3.3

module load r-project/3.3.3

Code Block

language	bash
title	R 3.4.2

module load r-project/3.4.2

Code Block

language	bash
title	R 3.4.3

module load anaconda/python3

Code Block

language	bash
title	R 3.5.3

module load r-project/3.5.3

Code Block

language	bash
title	r 3.5.3 for Bioinformatics

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

Code Block

language	bash

mkdir -p ${R_LIBS}

Start interactive R session and install package using the command

Code Block

language	bash

install.packages('packagename')

Alternatively, you can add install.packages('packagename') within your R script

Package List

34.02.7-1

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	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
cliprcaret	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	0.5.00
foreach	1.4.07	01.5.01
foreign	0.	clisymbols8-72	0.8-80
foreign	0.8-81	0.8-80
formatR	1.2.07	1.7
Formula	1.2.0-3
fs	1.3.1	1.25.0
clusterfutile.logger	21.04.532
futile.0.6options2	1.0.621
future	1.14.0
future.7-1	apply	1.3.0	codetools
gbRd	0.24-15	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	rcmdcheck11
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

.0.0RcppArmadillo.8.100

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	1.30.20
RColorBrewerxtable	1.18-24	1.18-2	1.1-2	1.1-2	Rcpp4
xts	0.11-2	0.12.151
XVector	0.1224.130
yaml	02.122.1401	2.02.01
zeallot	0	.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
zip	2.0.3
zlibbioc	1.30.0
zoo	1.8-6	1.8-8

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

Code Block

language	bash

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

Code Block

language	bash

install.packages('packagename',lib=Sys.getenv("R_LIBS"))

Expand

title	Deprecated CentOS 7.x Software: Use module load cent7 to use the following modules

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

Code Block

language	bash
title	R 3.3.3

module load r-project/3.3.3

Code Block

language	bash
title	R 3.4.2

module load r-project/3.4.2

Code Block

language	bash
title	R 3.4.3

module load anaconda/python3

Code Block

language	bash
title	R 3.5.3

module load r-project/3.5.3

Code Block

language	bash
title	r 3.5.3 for Bioinformatics

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

Code Block

language	bash

mkdir -p ${R_LIBS}

Start interactive R session and install package using the command

Code Block

language	bash

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

Code Block

language	bash

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

...

xfun

...

0.6

...

0.6

...

0.5

...

xml2

...

.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

...

xts

...

0.11-2

...

0.10-1

...

0.10-1

...

yaml

...

2.1.16

...

2.1.14

...

2.1.16

...

2.2.0

...

.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

...

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

Code Block

language	bash

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

Code Block

language	bash

install.packages('packagename',lib=Sys.getenv("R_LIBS"))

.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

Versions Compared

Old Version 16

New Version 17

Key

Installed Packages

Installed Packages

Which versions of R are available?

Usage

How to install R packages?

How to install R packages?

Which versions of R are available?

Usage

How to install R packages?

Installed Packages

Installed Packages

How to install R packages?