source("http://bioconductor.org/biocLite.R")

courseRepos <- "http://bioconductor.org/course-packages"
allRepos <- c(courseRepos, biocinstallRepos())

allPkgs <-
  c("HTSandGeneCentricLabs",
    "IRanges", "GenomicRanges", "Biostrings", "BSgenome", "rtracklayer",
    "biomaRt", "GenomicFeatures", "Rsamtools", "ShortRead",
    "EatonEtAlChIPseq", "leeBamViews", "RSQLite", "GO.db", "KEGG.db", "RCurl",
    "org.Sc.sgd.db", "yeast2.db", "yeast2probe", "ygs98probe",
    "BSgenome.Scerevisiae.UCSC.sacCer2", "org.Hs.eg.db", "hgu95av2.db")

update.packages(repos = allRepos, ask = FALSE)

newPkgs <- setdiff(allPkgs, installed.packages())

if (length(newPkgs) > 0)
    install.packages(newPkgs, repos = allRepos)