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# adapted from http://stackoverflow.com/questions/4090169/elegant-way-to-check-for-missing-packages-and-install-them
# adapted from @roryk https://github.com/roryk/bcbio.rnaseq/blob/master/resources/scripts/install_libraries.R
library(methods)
mirror = "http://cran.at.r-project.org"
update.packages(checkBuilt = TRUE, ask = FALSE, repos=mirror)
is_package_installed = function(package) {
available = suppressMessages(suppressWarnings(sapply(package, require,
quietly = TRUE, character.only = TRUE, warn.conflicts = FALSE)))
missing = package[!available]
if (length(missing) > 0) return(FALSE)
return(TRUE)
}
install.cran = function(packages, default_mirror="http://cran.at.r-project.org") {
for(i in packages) {
# require returns TRUE invisibly if it was able to load package
if(!is_package_installed(i)) {
options(repos = c(CRAN = default_mirror))
suppressMessages(suppressWarnings(install.packages(i, dependencies = TRUE, repo=default_mirror)))
}
}
}
install.bioconductor = function(packages, default_mirror="http://cran.at.r-project.org") {
for(i in packages) {
# require returns TRUE invisibly if it was able to load package
if(!is_package_installed(i)) {
suppressMessages(suppressWarnings(biocLite(i, ask=FALSE)))
}
}
}
install.github = function(package, branch="master") {
library(devtools)
for(i in packages) {
suppressMessages(suppressWarnings(install_github(package, ref=branch)))
}
}
cran_packages = c("devtools", "ggplot2", "reshape", "dplyr", "knitr", "gplots", "gridExtra", "pheatmap", "gtools")
install.cran(cran_packages)
bioconductor_packages = c("edgeR", "HTSFilter", "DESeq2", "DEGreport)
source("http://bioconductor.org/biocLite.R")
install.bioconductor(bioconductor_packages)
# novel packages
install.github("hbc/CHBUtils")
install.github("lpantano/isomiRs", "master")
install_github('rstudio/rmarkdown')
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