EBSeq/BiocInstaller/scripts/biocLite.R

   1 ## Mirrors: uncomment the following and change to your favorite CRAN mirror
   2 ## if you don't want to use the default (cran.fhcrc.org, Seattle, USA).
   3 ## options("repos" = c(CRAN="http://cran.fhcrc.org"))
   4
   5 ## Mirrors: uncomment the following and change to your favorite Bioconductor
   6 ## mirror, if you don't want to use the default (www.bioconductor.org,
   7 ## Seattle, USA)
   8 ## options("BioC_mirror" = "http://www.bioconductor.org")
   9
  10 local({
  11     currBiocVers <-
  12         package_version(readLines("http://bioconductor.org/bioc-version",
  13         warn=FALSE))
  14     vers <- getRversion()
  15     biocVers <- tryCatch({
  16         BiocInstaller::biocVersion() # recent BiocInstaller
  17     }, error=function(...) {         # no / older BiocInstaller
  18         tools:::.BioC_version_associated_with_R_version
  19     })
  20
  21     if (biocVers < currBiocVers) {
  22         txt <- strwrap(sprintf("Your Bioconductor is out-of-date, upgrade
  23             to version %s by following instructions at
  24             http://bioconductor.org/install.", currBiocVers))
  25         message(paste(txt, collapse="\n"))
  26     }
  27
  28     if (vers > "2.13" && biocVers > "2.8") {
  29
  30         if (exists("biocLite", .GlobalEnv, inherits=FALSE)) {
  31             txt <- strwrap("There is an outdated biocLite() function in the
  32                 global environment; run 'rm(biocLite)' and try again.")
  33             stop("\n", paste(txt, collapse="\n"))
  34         }
  35
  36         if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) {
  37             a <- NULL
  38             p <- file.path(Sys.getenv("HOME"), ".R", "repositories")
  39             if (file.exists(p)) {
  40                 a <- tools:::.read_repositories(p)
  41                 if (!"BioCsoft" %in% rownames(a))
  42                     a <- NULL
  43             }
  44             if (is.null(a)) {
  45                 p <- file.path(R.home("etc"), "repositories")
  46                 a <- tools:::.read_repositories(p)
  47             }
  48             if (!"package:utils" %in% search()) {
  49                 url <- "http://bioconductor.org/biocLite.R"
  50                 txt <- sprintf("use 'source(\"%s\")' to update 'BiocInstaller'
  51                                 after 'utils' package is attached",
  52                                url)
  53                 message(paste(strwrap(txt), collapse="\n  "))
  54             } else {
  55                 ## add a conditional for Bioc releases occuring WITHIN
  56                 ## a single R minor version
  57                 if (vers >= "2.15" && vers < "2.16") {
  58                     a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.11",
  59                       a["BioCsoft", "URL"])
  60                     biocVers <- numeric_version("2.11")
  61                 }
  62                 install.packages("BiocInstaller", repos=a["BioCsoft", "URL"])
  63                 if (!suppressWarnings(require("BiocInstaller",
  64                                               quietly=TRUE))) {
  65                     url0 <- "http://www.bioconductor.org/packages"
  66                     url <- sprintf("%s/%s/bioc",
  67                                    url0, as.character(biocVers))
  68                     txt0 <- "'biocLite.R' failed to install 'BiocInstaller',
  69                             use 'install.packages(\"%s\", repos=\"%s\")'"
  70                     txt <- sprintf(txt0, "BiocInstaller", url)
  71                     message(paste(strwrap(txt), collapse="\n  "))
  72                 }
  73             }
  74         }
  75     } else {
  76         source("http://bioconductor.org/getBioC.R")
  77         biocLite <<-
  78             function(pkgs, groupName="lite", ...)
  79             {
  80                 if (missing(pkgs))
  81                     biocinstall(groupName=groupName, ...)
  82                 else
  83                     biocinstall(pkgs=pkgs, groupName=groupName, ...)
  84             }
  85     }
  86 })