Package Management Quick Reference
Andy Lathrop
March 23, 2016
Built with Microsoft R Open version 3.2.3. More info at https://mran.revolutionanalytics.com/open/
The current CRAN repository for packages is https://mran.revolutionanalytics.com/snapshot/2016-01-01
Setup options: echo means R code will be displayed | cache means results will be stored for future knits
knitr::opts_chunk$set(echo = TRUE, cache = TRUE)Admin notes
This is an R markdown document and requires the ‘rmarkdown’ package
install.packages('rmarkdown', repos='http://cran.us.r-project.org')## Warning: package 'rmarkdown' is in use and will not be installedlibrary(rmarkdown)Package management utilities
The list of CRAN mirrors can be found at https://cran.r-project.org/mirrors.html
Repo used by current R session
getOption("repos")## CRAN
## "https://mran.revolutionanalytics.com/snapshot/2016-01-01"Current local library
normalizePath(.libPaths(), winslash = "/")## [1] "C:/Program Files/Microsoft/MRO/R-3.2.3/library"Local library of packages
installed.packages()[, "Package"]## assertthat base base64enc BB
## "assertthat" "base" "base64enc" "BB"
## BH bitops boot brew
## "BH" "bitops" "boot" "brew"
## caTools checkpoint class cluster
## "caTools" "checkpoint" "class" "cluster"
## codetools colorspace compiler crayon
## "codetools" "colorspace" "compiler" "crayon"
## curl datasets DBI devtools
## "curl" "datasets" "DBI" "devtools"
## dfoptim dichromat digest doParallel
## "dfoptim" "dichromat" "digest" "doParallel"
## dplyr e1071 evaluate foreach
## "dplyr" "e1071" "evaluate" "foreach"
## forecast foreign formatR Formula
## "forecast" "foreign" "formatR" "Formula"
## fracdiff gam gbm ggfortify
## "fracdiff" "gam" "gbm" "ggfortify"
## ggplot2 git2r glmnet graphics
## "ggplot2" "git2r" "glmnet" "graphics"
## grDevices grid gridBase gridExtra
## "grDevices" "grid" "gridBase" "gridExtra"
## gtable highr HSAUR2 htmltools
## "gtable" "highr" "HSAUR2" "htmltools"
## httr igraphdata irlba ISLR
## "httr" "igraphdata" "irlba" "ISLR"
## iterators jsonlite KernSmooth knitr
## "iterators" "jsonlite" "KernSmooth" "knitr"
## labeling lattice latticeExtra lazyeval
## "labeling" "lattice" "latticeExtra" "lazyeval"
## leaps magrittr markdown MASS
## "leaps" "magrittr" "markdown" "MASS"
## Matrix MatrixModels memoise methods
## "Matrix" "MatrixModels" "memoise" "methods"
## mgcv mime munsell nlme
## "mgcv" "mime" "munsell" "nlme"
## NLP nnet numDeriv openssl
## "NLP" "nnet" "numDeriv" "openssl"
## optextras packrat pacman parallel
## "optextras" "packrat" "pacman" "parallel"
## pkgmaker PKI PKPDmodels plyr
## "pkgmaker" "PKI" "PKPDmodels" "plyr"
## praise quadprog R6 randomForest
## "praise" "quadprog" "R6" "randomForest"
## Rcgmin RColorBrewer Rcpp RcppArmadillo
## "Rcgmin" "RColorBrewer" "Rcpp" "RcppArmadillo"
## RCurl registry reshape reshape2
## "RCurl" "registry" "reshape" "reshape2"
## RevoUtilsMath rgenoud RJSONIO rmarkdown
## "RevoUtilsMath" "rgenoud" "RJSONIO" "rmarkdown"
## rngtools roxygen2 rpart rsconnect
## "rngtools" "roxygen2" "rpart" "rsconnect"
## rstudioapi rversions Rvmmin sandwich
## "rstudioapi" "rversions" "Rvmmin" "sandwich"
## scales setRNG spatial splines
## "scales" "setRNG" "spatial" "splines"
## stats stats4 stringi stringr
## "stats" "stats4" "stringi" "stringr"
## survival svUnit tcltk TH.data
## "survival" "svUnit" "tcltk" "TH.data"
## tidyr timeDate tools translations
## "tidyr" "timeDate" "tools" "translations"
## tree tseries TTR utils
## "tree" "tseries" "TTR" "utils"
## whisker withr xml2 xtable
## "whisker" "withr" "xml2" "xtable"
## xts yaml zoo
## "xts" "yaml" "zoo"Choose CRAN mirror site from list
(remove # to run code)
# chooseCRANmirror()Choose a CRAN repo via URL
options(repos=structure(c(CRAN="http://cran.us.r-project.org")))Install from a particular mirror
install.packages('rmarkdown', repos='http://cran.us.r-project.org')## Warning: package 'rmarkdown' is in use and will not be installedPermanently set CRAN repo
(does not work with Microsoft R distro)
local({
r <- getOption("repos")
r["CRAN"] <- "http://cran.us.r-project.org"
options(repos = r)
})Add CRAN repos
(remove # to run code)
# setRepositories(addURLs =
# c(CRANxtras = "http://cran.us.r-project.org"))
# setRepositories(addURLs =
# c(CRAN = "http://cran.us.r-project.org"))Packages w/ newer versions available
old.packages()## NULLAbout using Microsoft R distribution
Microsoft uses the MRAN repo for packages, usually a snapshot of the Austria CRAN repo from the first of the month
(more info at https://mran.revolutionanalytics.com/timemachine/ )
The ‘checkpoint’ package from MSFT is helpful for using a specific repo snapshot more info at http://bit.ly/1Rzrqdy
- When you create a checkpoint, the checkpoint() function performs the following:
- Creates a snapshot folder to install packages. This library folder is located at ~/.checkpoint
- Scans your project folder for all packages used. Specifically, it searches for all instances of library() and requires() in your code.
- Installs these packages from the MRAN snapshot into your snapshot folder using install.packages()
- Sets options for your CRAN mirror to point to a MRAN snapshot, i.e. modify options(repos)
This means the remainder of your script will run with the packages from a specific date.
