OS: WIN7
R: 3.02
RStudio: 0.98.312
1. Install R
R is available at http://www.r-project.org/.
2. Update R
if (!require(installr)) {
# load / install+load installr
install.packages("installr")
require(installr)
}
updateR()
3. Install R packages
3.1 Installing R packages from CRAN (http://cran.r-project.org/)
install.packages("FinCal", dependencies = TRUE) # FinCal is the package name
or
RStudio -> Tools -> Install Packages -> Install from 'Repository (CRAN)'
3.2 Installing R packages from Package Archive File (offline)
install.packages("FinCal_0.5.zip")
or
RStudio -> Tools -> Install Packages -> Install from 'Package Archive File'
or
R CMD INSTALL FinCal_0.5.zip
3.3 Installing R packages from Bioconductor (http://www.bioconductor.org/)
source("http://bioconductor.org/biocLite.R") # installs 'BiocInstaller'
biocLite() # installs automatically 'Biobase' 'IRanges' 'AnnotationDbi' ‘BiocGenerics’ ‘RSQLite’
all_group() # Get list of all packages in BioConductor
biocLite(c("GenomicFeatures", "AnnotationDbi")) #installing GenomicFeatures &AnnotationDbi packages
3.4 Installing R packages from GitHub (https://github.com/)
install.packages("devtools") # requires for downloading & installation of GitHub packages
require(devtools)
install_github(repo = "FinCal", username = "felixfan") # installing FinCal package
4. Update all existing packages
4.1 Automated Re-Install of Packages (packages in the default library dir)
update.packages(ask = FALSE, repos = "http://cran.rstudio.org", checkBuilt = TRUE)
or just
update.packages(ask = FALSE)
4.2 Automated Re-Install of Packages (packages do not in the default library dir)
.libPaths() # gets the library trees within which packages are looked for
myPath = c("C:/Users/alice/Documents/R/win-library/3.0") # change it to your own dir
package_df <- as.data.frame(installed.packages(myPath)) #Get currently installed packages
package_list <- as.character(package_df$Package)
install.packages(package_list) #Re-install all installed packages
5. Reference
Installing R packages from CRAN/Bioconductor/Omegahat/Github
R 3.0.0 is released! (what’s new, and how to upgrade)
Automated Re-Install of Packages for R 3.0