R/mirrored/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
  12     vers <- getRversion()
  13     biocVers <- tryCatch({
  14         BiocInstaller::biocVersion() # recent BiocInstaller
  15     }, error=function(...) {         # no / older BiocInstaller
  16         BioC_version_associated_with_R_version <-
  17             get(".BioC_version_associated_with_R_version",
  18                 envir=asNamespace("tools"), inherits=FALSE)
  19         if (is.function(BioC_version_associated_with_R_version))
  20             BioC_version_associated_with_R_version()
  21         else                            # numeric_version
  22             BioC_version_associated_with_R_version
  23     })
  24
  25     if (vers < "3.0") {
  26         ## legacy; no need to change "3.0" ever
  27         ## coordinate this message with .onAttach
  28         txt <- strwrap("A new version of Bioconductor is available
  29             after installing the most recent version of R; see
  30             http://bioconductor.org/install", exdent=2)
  31         message(paste(txt, collapse="\n"))
  32     } else if ("package:BiocInstaller" %in% search()) {
  33         ## messages even if already attached
  34         tryCatch(BiocInstaller:::.onAttach(), error=function(...) NULL)
  35     }
  36
  37     if (vers > "2.13" && biocVers > "2.8") {
  38
  39         if (exists("biocLite", .GlobalEnv, inherits=FALSE)) {
  40             txt <- strwrap("There is an outdated biocLite() function in the
  41                 global environment; run 'rm(biocLite)' and try again.")
  42             stop("\n", paste(txt, collapse="\n"))
  43         }
  44
  45         if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) {
  46             a <- NULL
  47             p <- file.path(Sys.getenv("HOME"), ".R", "repositories")
  48             if (file.exists(p)) {
  49                 a <- tools:::.read_repositories(p)
  50                 if (!"BioCsoft" %in% rownames(a))
  51                     a <- NULL
  52             }
  53             if (is.null(a)) {
  54                 p <- file.path(R.home("etc"), "repositories")
  55                 a <- tools:::.read_repositories(p)
  56             }
  57             if (!"package:utils" %in% search()) {
  58                 url <- "http://bioconductor.org/biocLite.R"
  59                 txt <- sprintf("use 'source(\"%s\")' to update 'BiocInstaller'
  60                                 after 'utils' package is attached",
  61                                url)
  62                 message(paste(strwrap(txt), collapse="\n  "))
  63             } else {
  64                 ## add a conditional for Bioc releases occuring WITHIN
  65                 ## a single R minor version. This is so that a user with a
  66                 ## version of R (whose etc/repositories file references the
  67                 ## no-longer-latest URL) and without BiocInstaller
  68                 ## will be pointed to the most recent repository suitable
  69                 ## for their version of R
  70                 if (vers == "3.2.0") {
  71                     a["BioCsoft", "URL"] <- sub(as.character(biocVers), "3.1",
  72                       a["BioCsoft", "URL"])
  73                 } else if (vers == "3.1.1") {
  74                     ## R-3.1.1's etc/repositories file at the time of the release
  75                     ## of Bioc 3.0 pointed to the 2.14 repository, but we want
  76                     ## new installations to access the 3.0 repository
  77                     a["BioCsoft", "URL"] <- sub(as.character(biocVers), "3.0",
  78                       a["BioCsoft", "URL"])
  79                 } else if (vers == "3.1.0") {
  80                     ## R-devel points to 2.14 repository
  81                     a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.14",
  82                       a["BioCsoft", "URL"])
  83                 } else if (vers >= "2.15" && vers < "2.16") {
  84                     a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.11",
  85                       a["BioCsoft", "URL"])
  86                     biocVers <- numeric_version("2.11")
  87                 }
  88                 install.packages("BiocInstaller", repos=a["BioCsoft", "URL"])
  89                 if (!suppressWarnings(require("BiocInstaller",
  90                                               quietly=TRUE))) {
  91                     url0 <- "http://www.bioconductor.org/packages"
  92                     url <- sprintf("%s/%s/bioc",
  93                                    url0, as.character(biocVers))
  94                     txt0 <- "'biocLite.R' failed to install 'BiocInstaller',
  95                             use 'install.packages(\"%s\", repos=\"%s\")'"
  96                     txt <- sprintf(txt0, "BiocInstaller", url)
  97                     message(paste(strwrap(txt), collapse="\n  "))
  98                 }
  99             }
 100         } else {
 101              ## BiocInstaller version 1.16.0-1.18.1 do not
 102              ## automatically update when type=="source"; notify users
 103              ## when they have updated R over their old libraries
 104              installerVersion <- utils::packageVersion("BiocInstaller")
 105              test0 <- (vers > "3.1.2") &&
 106                  !identical(getOption("pkgType"), "source") &&
 107                      (installerVersion >= "1.16.0") &&
 108                          (installerVersion <= "1.16.4")
 109              if (test0) {
 110                  if (installerVersion < "1.16.4") {
 111                      txt <- "Update BiocInstaller with
 112                          oldPkgType=options(pkgType=\"source\");
 113                          biocLite(\"BiocInstaller\"); options(oldPkgType)"
 114                      message(paste(strwrap(txt, exdent=2), collapse="\n"))
 115                  }
 116                  if (vers >= "3.2") {
 117                      txt <- sprintf("BiocInstaller version %s is too old for
 118                      R version %s; remove.packages(\"BiocInstaller\"),
 119                      re-start R, then
 120                      source(\"http://bioconductor.org/biocLite.R\")",
 121                                     biocVers, vers)
 122                      warning(paste(strwrap(txt, exdent=2), collapse="\n"))
 123                  }
 124              }
 125          }
 126     } else {
 127         source("http://bioconductor.org/getBioC.R")
 128         biocLite <<-
 129             function(pkgs, groupName="lite", ...)
 130             {
 131                 if (missing(pkgs))
 132                     biocinstall(groupName=groupName, ...)
 133                 else
 134                     biocinstall(pkgs=pkgs, groupName=groupName, ...)
 135             }
 136     }
 137 })