Use PATH env to instead the variable

[rsem.git] / EBSeq / BiocInstaller / scripts / biocLite.R

diff --git a/EBSeq/BiocInstaller/scripts/biocLite.R b/EBSeq/BiocInstaller/scripts/biocLite.R
deleted file mode 100644 (file)
index 9940cfb..0000000
--- a/EBSeq/BiocInstaller/scripts/biocLite.R
+++ /dev/null
@@ -1,86 +0,0 @@
-## Mirrors: uncomment the following and change to your favorite CRAN mirror
-## if you don't want to use the default (cran.fhcrc.org, Seattle, USA).
-## options("repos" = c(CRAN="http://cran.fhcrc.org"))
-
-## Mirrors: uncomment the following and change to your favorite Bioconductor
-## mirror, if you don't want to use the default (www.bioconductor.org,
-## Seattle, USA)
-## options("BioC_mirror" = "http://www.bioconductor.org")
-
-local({
-    currBiocVers <- 
-        package_version(readLines("http://bioconductor.org/bioc-version",
-        warn=FALSE))
-    vers <- getRversion()
-    biocVers <- tryCatch({
-        BiocInstaller::biocVersion() # recent BiocInstaller
-    }, error=function(...) {         # no / older BiocInstaller
-        tools:::.BioC_version_associated_with_R_version
-    })
-
-    if (biocVers < currBiocVers) {
-        txt <- strwrap(sprintf("Your Bioconductor is out-of-date, upgrade
-            to version %s by following instructions at
-            http://bioconductor.org/install.", currBiocVers))
-        message(paste(txt, collapse="\n"))
-    }
-
-    if (vers > "2.13" && biocVers > "2.8") {
-
-        if (exists("biocLite", .GlobalEnv, inherits=FALSE)) {
-            txt <- strwrap("There is an outdated biocLite() function in the
-                global environment; run 'rm(biocLite)' and try again.")
-            stop("\n", paste(txt, collapse="\n"))
-        }
-          
-        if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) {
-            a <- NULL
-            p <- file.path(Sys.getenv("HOME"), ".R", "repositories")
-            if (file.exists(p)) {
-                a <- tools:::.read_repositories(p)
-                if (!"BioCsoft" %in% rownames(a)) 
-                    a <- NULL
-            }
-            if (is.null(a)) {
-                p <- file.path(R.home("etc"), "repositories")
-                a <- tools:::.read_repositories(p)
-            }
-            if (!"package:utils" %in% search()) {
-                url <- "http://bioconductor.org/biocLite.R"
-                txt <- sprintf("use 'source(\"%s\")' to update 'BiocInstaller'
-                                after 'utils' package is attached",
-                               url)
-                message(paste(strwrap(txt), collapse="\n  "))
-            } else {
-                ## add a conditional for Bioc releases occuring WITHIN
-                ## a single R minor version
-                if (vers >= "2.15" && vers < "2.16") {
-                    a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.11",
-                      a["BioCsoft", "URL"])
-                    biocVers <- numeric_version("2.11")
-                }
-                install.packages("BiocInstaller", repos=a["BioCsoft", "URL"])
-                if (!suppressWarnings(require("BiocInstaller",
-                                              quietly=TRUE))) {
-                    url0 <- "http://www.bioconductor.org/packages"
-                    url <- sprintf("%s/%s/bioc",
-                                   url0, as.character(biocVers))
-                    txt0 <- "'biocLite.R' failed to install 'BiocInstaller',
-                            use 'install.packages(\"%s\", repos=\"%s\")'"
-                    txt <- sprintf(txt0, "BiocInstaller", url)
-                    message(paste(strwrap(txt), collapse="\n  "))
-                }
-            }
-        }
-    } else {
-        source("http://bioconductor.org/getBioC.R")
-        biocLite <<-
-            function(pkgs, groupName="lite", ...)
-            {
-                if (missing(pkgs))
-                    biocinstall(groupName=groupName, ...)
-                else
-                    biocinstall(pkgs=pkgs, groupName=groupName, ...)
-            }
-    }
-})