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

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. 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

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"))

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

R 3.3.3

module load r-project/3.3.3

R 3.4.2

module load r-project/3.4.2

R 3.4.3

module load anaconda/python3

R 3.5.3

module load r-project/3.5.3

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

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