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install.R
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install.R
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################################################################################
# Check that the currently-installed version of R
# is at least the minimum required version.
################################################################################
R_min_version = "3.6.0"
R_version = paste0(R.Version()$major, ".", R.Version()$minor)
if(compareVersion(R_version, R_min_version) < 0){
stop("You do not have the latest required version of R installed.\n",
"Launch should fail.\n",
"Go to http://cran.r-project.org/ and update your version of R.")
}
# install or update BiocManager. Updates sometimes needed as they change in-step with BioC vers
install.packages("BiocManager")
################################################################################
# Install basic required packages if not available/installed.
################################################################################
install_missing_packages = function(pkg, version = NULL, verbose = TRUE){
availpacks = .packages(all.available = TRUE)
require("BiocManager")
missingPackage = FALSE
if(!any(pkg %in% availpacks)){
if(verbose){
message("The following package is missing.\n",
pkg, "\n",
"Installation will be attempted...")
}
missingPackage <- TRUE
}
if(!is.null(version) & !missingPackage){
# version provided and package not missing, so compare.
if( compareVersion(a = as.character(packageVersion(pkg)),
b = version) < 0 ){
if(verbose){
message("Current version of package\n",
pkg, "\t",
packageVersion(pkg), "\n",
"is less than required.
Update will be attempted.")
}
missingPackage <- TRUE
}
}
if(missingPackage){
BiocManager::install(pkg, update=FALSE)
}
}
################################################################################
# Define list of package names and required versions.
################################################################################
deppkgs = c(phyloseq = "1.16.0",
biomformat = "1.0.0",
shiny = "0.13.2",
shinythemes = "1.0.1",
ggplot2 = "2.1.0",
data.table = "1.9.6",
networkD3 = "0.2.10",
genefilter = "1.54.0",
grid = "3.3.0",
gridExtra = "2.2.1",
markdown = "0.7.7",
rmarkdown = "0.9.6",
png = "0.1.7",
RColorBrewer = "1.1.2",
scales = "0.4.0")
# Loop on package check, install, update
pkg1 = mapply(install_missing_packages,
pkg = names(deppkgs),
version = deppkgs,
MoreArgs = list(verbose = TRUE),
SIMPLIFY = FALSE,
USE.NAMES = TRUE)
################################################################################
# Load packages that must be fully-loaded
################################################################################
for(i in names(deppkgs)){
library(i, character.only = TRUE)
message(i, " package version:\n", packageVersion(i))
}
################################################################################