R/load_required_bioconductor_packages.R

In elqumsan/RNAseqMVA: Application of Multivariate Analysis methods to RNA-seq Data

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################### Required Library #############################
##################################################################

#' @title Load required packages from BioConductor, afte having installed them if necessary.
#' @author Mustafa AbuElQumsan and Jacques van Helden
#' @description Load a list of required BioConductor packages. For each specified package,
#' first check  if it is available on this R instance. If not, automatically install it.
#' @param packages a vector containing a list of required BioConductor packages.
#' @return chack and then install all BioConductor packages if it aren't installed.
#' @export
LoadRequiredBioconductorPackages <- function(packages, verbose = 0) {
  for (pkg in packages) {
    if (!require(pkg, character.only = TRUE)) {
      if (verbose >= 1) { message("\tInstalling required BioConductor library\t", pkg) }

      if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
      BiocManager::install

      BiocManager::install(pkgs = pkg, ask = FALSE)


      # source('http://bioconductor.org/biocLite.R')
      # # biocLite("BiocUpgrade") # note: I had to add this
      # biocLite(pkg)
    }
    if (verbose >= 1) { message("\tLoading required BioConductor library\t", pkg) }
    library(pkg, character.only = TRUE)
  }
}

## Check validity of Bioconductor installation
# BiocManager::valid()