updating full set of installed packages in R

updatePackagesScript.R

# list of github installed packages
#gitPackages <- list(c("devtools", "hadley"),
#                    c("samatha", "DASpringate"),
#                    c("twitteR", "geoffjentry"))

# Other specific things

# list of local packages
localPackages <- c("~/Projects/work/rmfNotifier")

# get previous set of installed packages
oldLib <- "/home/rmflight/R-322-bioc-31-libs"
newLib <- "/home/rmflight/R-331-bioc-33-libs"
allInstalled <- installed.packages(oldLib)
newInstalled <- installed.packages(newLib)

if (length(list.files(newLib)) > 0){
  tryInstall <- setdiff(rownames(allInstalled), rownames(newInstalled))
} else {
  tryInstall <- rownames(allInstalled)
}

  
# get the dependencies
allDeps <- tools:::package_dependencies(tryInstall, db = allInstalled)

nDep <- vapply(allDeps, function(x){
  retVal <- 0
  if (!(is.null(x))){
    retVal <- length(x)
  }
  retVal
}, double(1))

nDep <- sort(nDep, decreasing = FALSE)
toInstall <- names(nDep)

cranRepo <- "https://cran.rstudio.com/"
cranAvailable <- available.packages(contrib.url(cranRepo))
isCran <- toInstall[toInstall %in% rownames(cranAvailable)]

for (package in isCran){
  install.packages(package, repo=cranRepo, lib = newLib)
  wasInstalled <- toInstall %in% rownames(installed.packages(newLib))
}
  
biocRepos <- c("https://bioconductor.org/packages/3.3/bioc/src/contrib",
               "https://bioconductor.org/packages/3.3/data/experiment/src/contrib",
               "https://bioconductor.org/packages/3.3/data/annotation/src/contrib",
               "https://bioconductor.org/packages/3.3/extra/src/contrib")


biocAvailable <- available.packages(biocRepos)
isBioc <- toInstall[toInstall %in% rownames(biocAvailable)]

for (package in isBioc){
  install.packages(package, contriburl = biocRepos, lib = newLib)
  wasInstalled <- toInstall %in% rownames(installed.packages(newLib))
}