Installing R packages in lab

[dlondon]

Just wondering if anyone has some pointers or ideas on how you install R packages for lab use? Most of of what I see describes installing via the R console

I’m also wondering if there is a way to install directly from the repositories

What I really want to do is script it so that I can just deploy using Jamf Pro

[Reno · Accepted solution]

Here's one I used a while back.

#!/usr/local/bin/Rscript

args <- commandArgs(TRUE)


if(length(args[]) < 4) {
    print("Must include at least one package for installation")
    q()
}


#First three arguements are reserved for the JSS.  Get rid of them...
args <- args[-1]
args <- args[-1]
args <- args[-1]




for(currentPackage in args) {
    message("Installing: ", currentPackage )
    if(!require(currentPackage,character.only = TRUE)){
        message("Installing: ", currentPackage )
        install.packages(currentPackage , dependencies = TRUE, repos='http://cran.us.r-project.org')
    }else{
        message("Package ", currentPackage, " is already installed")
    }
}

q()

[dlondon]

Thanks @Reno (Brad) - that helps massively. I have somewhere around 300 packages that were requested so I'll do some reading and see if I can add something like a here doc in Bash to Rscript.

Thanks for lifting the lid - much appreciated

Regards,
David

[dlondon]

This is what I came up with:

#!/bin/bash
# Install_R_Package.bash
# 2020-06-22 David London
# Credit and Inspiration - Brad Reno https://www.jamf.com/jamf-nation/discussions/35969/installing-r-packages-in-lab

# path to Rscript script that installs the packages
script="/tmp/Install_R_Package.R"
echo "creating /tmp/Install_R_Package.R"

# Create the Rscript file
echo "#!/usr/local/bin/Rscript" > "$script"
echo "# Install_R_Package.R" >> "$script"
echo "# https://www.jamf.com/jamf-nation/discussions/35969/installing-r-packages-in-lab" >> "$script"
echo >> "$script"
echo "args <- commandArgs(TRUE)" >> "$script"
echo >> "$script"
echo "if(length(args[]) < 1) {" >> "$script"
echo "    print(\"Must include at least one package for installation\")" >> "$script"
echo "    q()" >> "$script"
echo "}" >> "$script"
echo >> "$script"
echo "for(currentPackage in args) {" >> "$script"
echo "    message(\"Installing: \", currentPackage )" >> "$script"
echo "    if(!require(currentPackage,character.only = TRUE)){" >> "$script"
echo "        message(\"Installing: \", currentPackage )" >> "$script"
echo "        install.packages(currentPackage , dependencies = TRUE, repos='http://cran.us.r-project.org')" >> "$script"
echo "    }else{" >> "$script"
echo "        message(\"Package \", currentPackage, \" is already installed\")" >> "$script"
echo "    }" >> "$script"
echo "}" >> "$script"
echo >> "$script"
echo "q()" >> "$script"

echo "making /tmp/Install_R_Package.R executable"
chmod +x "$script"

# The list of packages required
packages=$(cat <<EOF
abind
acepack
addinslist
AER
akima
anytime
ape
aplpack
arm
askpass
assertthat
astro
audio
backports
base
base64enc
beepr
BH
bindr
bindrcpp
bitops
boot
brew
broom
BWStest
callr
car
carData
caTools
cellranger
checkmate
chron
class
classInt
cli
clipr
clisymbols
cluster
coda
codetools
coin
colorspace
colourpicker
combinat
commonmark
compiler
crayon
crosstalk
curl
data.table
DataExplorer
datasets
DBI
dbplyr
Dcchoice
DEoptimR
desc
DescTools
devtools
digest
dplyr
DT
e1071
effects
effsize
ellipsis
emmeans
EMT
estimability
evaluate
expm
fansi
fastICA
FNN
forcats
foreign
formatR
Formula
fs
gdata
gdistance
generics
geoR
geosphere
ggfittext
ggmap
ggplot2
ggThemeAssist
gh
git2r
glue
gmp
googlePolylines
googleway
graphics
grDevices
grid
gridExtra
gstat
gtable
gtools
gvlma
haven
hexbin
highr
Hmisc
hms
htmlTable
htmltools
htmlwidgets
httpuv
httr
igraph
ImportExport
ini
inspectdf
intervals
ipdw
jomo
jpeg
jqr
jsonlite
KernSmooth
klaR
knitr
kSamples
labeling
labelled
later
lattice
latticeExtra
lazyeval
lctools
libcoin
lme4
lmtest
lsmeans
magrittr
manipulateWidget
maptools
markdown
MASS
Matrix
matrixcalc
MatrixModels
matrixStats
memoise
methods
mgcv
mi
mice
mime
miniUI
minqa
mitml
mitools
modelr
modeltools
multcomp
multcompView
munsell
mvtnorm
networkD3
nlme
nloptr
nnet
nortest
numDeriv
nycflights13
openssl
OpenStreetMap
openxlsx
ordinal
pan
parallel
pbkrtest
PBSmapping
pillar
pkgbuild
pkgconfig
pkgload
plogr
plotrix
plyr
PMCMR
PMCMRplus
png
praise
prettymapr
prettyunits
processx
progress
proj4
promises
proto
ps
pscl
purrr
quantreg
questionr
R6
RandomFields
RandomFieldsUtils
rappdirs
raster
rcmdcheck
Rcmdr
RcmdrMisc
RColorBrewer
rcompanion
Rcpp
RcppEigen
readr
readstata13
readxl
relimp
rematch
remotes
reprex
reshape
reshape2
rgdal
rgeos
rgl
RgoogleMaps
rgr
rio
rJava
rjson
rlang
rmarkdown
Rmisc
Rmpfr
robustbase
RODBC
roxygen2
rpanel
rpart
rprojroot
rstudioapi
rvest
sandwich
scales
selectr
sem
sessioninfo
shades
shiny
shinyjs
soilphysics
soiltexture
soilwater
sourcetools
sp
spacetime
SparseM
spatial
spData
splancs
splines
stargazer
stats
stats4
stringi
stringr
SuppDists
survey
survival
sys
tcltk
tcltk2
testthat
TH.data
tibble
tidyr
tidyselect
tidyverse
tinytex
tkrplot
tools
translations
ucminf
usethis
utf8
utils
vctrs
vegan
viridis
viridisLite
webshot
weights
whisker
withr
wordcloud2
xfun
xlsx
xlsxjars
xml2
xopen
xtable
xts
yaml
zeallot
zip
zoo
EOF
)

# echo $packages

# Install the packages
for i in $packages
do
	echo "Attempting to install" $i
/usr/local/bin/Rscript $script $i
done

exit 0