Workspace management
Managing workspace packages.
Installing a package
From inside the workspace.
install.packages("knitr")
From outside any R session Download from CRAN, by ex. http://cran.r-project.org/web/packages/knitr/index.html
R CMD INSTALL knitr
Loading a package
Load a package, with or without the localisation to be used.
library("Biobase", lib.loc = "/home/chernan/R/i686-pc-linux-gnu-library/2.15")
List loaded packages
Get a global view of the current session. In reproducible research, this information is important to keep after a data analysis, in order to be able to re-set the same environment.
sessionInfo()
## R version 2.15.2 (2012-10-26)
## Platform: i686-pc-linux-gnu (32-bit)
##
## locale:
## [1] LC_CTYPE=fr_CH.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=fr_CH.UTF-8 LC_COLLATE=fr_CH.UTF-8
## [5] LC_MONETARY=fr_CH.UTF-8 LC_MESSAGES=fr_CH.UTF-8
## [7] LC_PAPER=C LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=fr_CH.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] datasets stats graphics grDevices utils methods base
##
## other attached packages:
## [1] biomaRt_2.14.0 ggplot2_0.9.3.1 markdown_0.5.4 knitr_1.1
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.2-1 dichromat_2.0-0 digest_0.6.3
## [4] evaluate_0.4.7 formatR_0.7 grid_2.15.2
## [7] gtable_0.1.2 KernSmooth_2.23-9 labeling_0.1
## [10] MASS_7.3-23 munsell_0.4 plyr_1.8
## [13] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-3
## [16] reshape2_1.2.2 scales_0.2.3 stringr_0.6.2
## [19] tools_2.15.2 XML_3.95-0.1
Get the list of all currently loaded packages, and a few information on them.
installed.packages()[.packages(), ]
## Package LibPath
## biomaRt "biomaRt" "/home/chernan/R/i686-pc-linux-gnu-library/2.15"
## ggplot2 "ggplot2" "/home/chernan/R/i686-pc-linux-gnu-library/2.15"
## markdown "markdown" "/home/chernan/R/i686-pc-linux-gnu-library/2.15"
## knitr "knitr" "/home/chernan/R/i686-pc-linux-gnu-library/2.15"
## datasets "datasets" "/usr/lib/R/library"
## stats "stats" "/usr/lib/R/library"
## graphics "graphics" "/usr/lib/R/library"
## grDevices "grDevices" "/usr/lib/R/library"
## utils "utils" "/usr/lib/R/library"
## methods "methods" "/usr/lib/R/library"
## base "base" "/usr/lib/R/library"
## Version Priority Depends
## biomaRt "2.14.0" NA "methods"
## ggplot2 "0.9.3.1" NA "R (>= 2.14), stats, methods"
## markdown "0.5.4" NA "R (>= 2.11.1)"
## knitr "1.1" NA "R (>= 2.14.1)"
## datasets "2.15.2" "base" NA
## stats "2.15.2" "base" NA
## graphics "2.15.2" "base" NA
## grDevices "2.15.2" "base" NA
## utils "2.15.2" "base" NA
## methods "2.15.2" "base" NA
## base "2.15.2" "base" NA
## Imports
## biomaRt "utils, XML, RCurl"
## ggplot2 "plyr (>= 1.7.1), digest, grid, gtable (>= 0.1.1), reshape2,\nscales (>= 0.2.3), proto, MASS"
## markdown NA
## knitr "evaluate (>= 0.4.3), digest, formatR (>= 0.3-4), markdown (>=\n0.4), stringr (>= 0.6), tools"
## datasets NA
## stats NA
## graphics "grDevices"
## grDevices NA
## utils NA
## methods "utils"
## base NA
## LinkingTo
## biomaRt NA
## ggplot2 NA
## markdown NA
## knitr NA
## datasets NA
## stats NA
## graphics NA
## grDevices NA
## utils NA
## methods NA
## base NA
## Suggests
## biomaRt "annotate"
## ggplot2 "quantreg, Hmisc, mapproj, maps, hexbin, maptools, multcomp,\nnlme, testthat"
## markdown "RCurl"
## knitr "testthat, rgl, codetools, R2SWF (>= 0.4), XML, RCurl, Rcpp\n(>= 0.10.0)"
## datasets NA
## stats NA
## graphics NA
## grDevices NA
## utils NA
## methods NA
## base NA
## Enhances OS_type License Built
## biomaRt NA NA "Artistic-2.0" "2.15.2"
## ggplot2 "sp" NA "GPL-2" "2.15.2"
## markdown NA NA "GPL-3" "2.15.2"
## knitr NA NA "GPL" "2.15.2"
## datasets NA NA "Part of R 2.15.2" "2.15.2"
## stats NA NA "Part of R 2.15.2" "2.15.2"
## graphics NA NA "Part of R 2.15.2" "2.15.2"
## grDevices NA NA "Part of R 2.15.2" "2.15.2"
## utils NA NA "Part of R 2.15.2" "2.15.2"
## methods NA NA "Part of R 2.15.2" "2.15.2"
## base NA NA "Part of R 2.15.2" "2.15.2"
Save/Load
Save the list of loaded packages in a file, and load packages from this file.
- Write the list of loaded packages in a file
instPackages <- installed.packages()[.packages(), ]
write.table(instPackages, "loadedPackages.txt", quote = TRUE)
- Load packages from a file
packagesToLoad <- read.table("loadedPackages.txt", header = TRUE, stringsAsFactors = FALSE)
apply(packagesToLoad, 1, FUN = function(aLib) {
library(package = aLib["Package"], lib.loc = aLib["LibPath"], character.only = TRUE)
})
Detach a package
Detach a package
detach("package:affy", unload = TRUE)
This work by Celine Hernandez is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.