Updated samtools to 0.1.19

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

diff --git a/EBSeq/BiocInstaller/scripts/biocLite.R b/EBSeq/BiocInstaller/scripts/biocLite.R
new file mode 100644 (file)
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+++ b/EBSeq/BiocInstaller/scripts/biocLite.R
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+## 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- strwrap(sprintf("Your Bioconductor is out-of-date, upgrade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- strwrap("There is an outdated biocLite() function in the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, ...)
+            }
+    }
+})