[BioC] Installation Problem on OS X
Marcus Davy
MDavy at hortresearch.co.nz
Tue Nov 23 23:30:55 CET 2004
Furthur to seans suggestions, I have had problems with the XML R package before, the getBioC() log looks like it is trying to install the source XML package, I think it should be installing the MACOS X binary XML package (XML_0.95-6.tgz). This can be installed from within R 2.0.1 from the menu "R Package installer" under "Packages&Data". Then try the getBioC() installation again.
* Installing *source* package 'XML' ...
> checking for gcc... no
> checking for cc... no
> checking for cc... no
> checking for cl... no
> configure: error: no acceptable C compiler found in $PATH
> See `config.log' for more details.
> ERROR: configuration failed for package 'XML'
> Note: Package XML not found in any known repository.
> Note: Package graph not found in any known repository.
> Note: Package Rgraphviz not found in any known repository.
marcus
>>> Sean Davis <sdavis2 at mail.nih.gov> 24/11/2004 8:13:12 AM >>>
It looks like at the very least there may not be xtools installed
(which has compilers, make, etc.). Therefore, nothing from source that
requires compilation will work without installing these. You should
probably hear from others, as well, but that looks to be at least part
of the problem. Also, if you want to install into the R framework
library, you must have administrator privileges (work using sudo).
Another option is to install into the home directory (choose 1 from the
first question below).
Sean
On Nov 23, 2004, at 1:27 PM, David Rocke wrote:
> I have students installing R and Bioconductor on their personal
> machines, and all the Mac users are having problems with
> Bioconductor. This is a transcript of an attempted installation. If
> anyone knows how to fix this, that would be great. I do not use a Mac
> myself and am not knowledgeable on the issues.
>
> Thanks,
> David Rocke
>
> R : Copyright 2004, The R Foundation for Statistical Computing
> Version 2.0.0 (2004-10-04), ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for a HTML browser interface to help.
> Type 'q()' to quit R.
>
> [Previously saved workspace restored]
>
>> source("http://www.bioconductor.org/getBioC.R")
>> getBioC()
> Running getBioC version 1.2.68....
> If you encounter problems, first make sure that
> you are running the latest version of getBioC()
> which can be found at: www.bioconductor.org/getBioC.R
>
> Please direct any concerns or questions to
> bioconductor at stat.math.ethz.ch.
>
> Please select an installation directory:
> 1:/Users/Michael/Library/R/library
> 2:/Library/Frameworks/R.framework/Resources/library
> Selection:
> Enter an item from the menu, or 0 to exit
> Selection: 2
> Loading required package: reposTools
> Loading required package: tools
> Note: You did not specify a download type. Using a default value of:
> Source
> This will be fine for almost all users
>
> Note: You did not specify a download type. Using a default value of:
> Source
> This will be fine for almost all users
>
> Note: You did not specify a download type. Using a default value of:
> Source
> This will be fine for almost all users
>
> [1] "Attempting to download XML from
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing XML"
> * Installing *source* package 'XML' ...
> checking for gcc... no
> checking for cc... no
> checking for cc... no
> checking for cl... no
> configure: error: no acceptable C compiler found in $PATH
> See `config.log' for more details.
> ERROR: configuration failed for package 'XML'
> Note: Package XML not found in any known repository.
> Note: Package graph not found in any known repository.
> Note: Package Rgraphviz not found in any known repository.
> [1] "Attempting to download geneplotter from
> http://www.bioconductor.org/repository/release1.5/package/Source"
> [1] "Download complete."
> [1] "Installing geneplotter"
> * Installing *source* package 'geneplotter' ...
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> Loading required package: Biobase
> Loading required package: tools
> [1] TRUE
> Loading required package: annotate
> [1] TRUE
> [1] "Makesense"
> [1] "Makesense"
> Warning message:
> In the method signature for function "Makesense", no definition for
> class(es): "exprSet" in: matchSignature(signature, fdef, where)
> [1] "Makesense"
> [1] "imageMap"
> [1] "imageMap"
> Warning message:
> In the method signature for function "imageMap", no definition for
> class(es): "connection" in: matchSignature(signature, fdef, where)
>
> ** help
>>>> Building/Updating help pages for package 'geneplotter'
> Formats: text html latex example
> GetColor text html latex example
> Makesense text html latex example
> alongChrom text html latex example
> amplicon.plot text html latex example
> missing link(s): esApply esApply
> cColor text html latex example
> cPlot text html latex example
> cScale text html latex example
> colorRampPalette text html latex example
> eset133a text html latex example
> identifyLines text html latex example
> imageMap text html latex example
> missing link(s): plotPlate
> make.chromOrd text html latex example
> openHtmlPage text html latex example
> plotChr text html latex example
> plotExpressionGraph text html latex example
> missing link(s): plot.graph plot.graph
> savepng text html latex example
> * DONE (geneplotter)
> chmod:
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/R.css:
> Operation not permitted
> [1] "Installation complete"
> Warning messages:
> 1: Installation of package XML had non-zero exit status in:
> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> 2:
> Package graph version 1.5.1 suggests XML
> in: resolve.depends(pkgInfo, repEntry, force, lib = lib,
> searchOptions =
> searchOptions,
> 3:
> Package Rgraphviz version 1.5.0 depends on graph
> in: resolve.depends(pkgInfo, repEntry, force, lib = lib,
> searchOptions =
> searchOptions,
> [1] "Attempting to download pamr from
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing pamr"
> * Installing *source* package 'pamr' ...
> ** libs
> /Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make:
> command
> not found
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/pamr'
> ** Restoring previous
> '/Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/pamr'
> ERROR: compilation failed for package 'pamr'
> Warning message:
> Installation of package pamr had non-zero exit status in:
> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> [1] "Attempting to download globaltest from
> http://www.bioconductor.org/repository/release1.5/package/Source"
> [1] "Download complete."
> [1] "Installing globaltest"
> * Installing *source* package 'globaltest' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Creating a new generic function for "names" in "globaltest"
> Creating a new generic function for "names<-" in "globaltest"
> Creating a new generic function for "scale" in "globaltest"
> Creating a new generic function for "plot" in "globaltest"
>
> ** help
>>>> Building/Updating help pages for package 'globaltest'
> Formats: text html latex example
> checkerboard text html latex example
> exampleX text html latex
> exampleY text html latex
> geneplot text html latex example
> globaltest text html latex example
> gt.barplot-class text html latex
> gt.result-class text html latex
> permutations text html latex example
> regressionplot text html latex example
> sampleplot text html latex example
> sampling text html latex example
> * DONE (globaltest)
> chmod:
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/R.css:
> Operation not permitted
> [1] "Installation complete"
>> From URL:
>> http://www.bioconductor.org/repository/release1.5/package/Source
> geneplotter version 1.5.2
> globaltest version 3.0.2
>
>> From URL: http://www.bioconductor.org//CRANrepository
> pamr version 1.23
>
> You have downloaded a default set of packages.
> If you wish to see other download options, please go to the URL:
> http://www.bioconductor.org/faq.html#getBioC
>> affy
> Error: Object "affy" not found
>> load(affy)
> Error in load(affy) : Object "affy" not found
>> library(affy)
> Error: syntax error
>>
>> library
> function (package, help, pos = 2, lib.loc = NULL, character.only =
> FALSE,
> logical.return = FALSE, warn.conflicts = TRUE, keep.source =
> getOption("keep.source.pkgs"),
> verbose = getOption("verbose"), version)
> {
> testRversion <- function(pkgInfo, pkgname) {
> current <- getRversion()
> if (length(Rdeps <- pkgInfo$Rdepends) > 1) {
> target <- Rdeps$version
> res <- eval(parse(text = paste("current", Rdeps$op,
> "target")))
> if (!res)
> stop(paste("This is R ", current, ", package ",
> sQuote(pkgname), " needs ", Rdeps$op, " ",
> target, sep = ""), call. = FALSE)
> }
> if (!is.null(built <- pkgInfo$Built)) {
> if (built$R < "2.0.0")
> stop("package ", sQuote(pkgname), " was built before R
> 2.0.0: please re-install it",
> call. = FALSE)
> if (built$R > current)
> warning(paste("package", sQuote(pkgname), "was built
> under R
> version",
> built$R), call. = FALSE)
> if (.Platform$OS.type == "unix") {
> platform <- built$Platform
> if (length(grep("\\w", platform))) {
> m <- agrep(platform, R.version$platform)
> if (!length(m))
> stop(paste("package", sQuote(pkgname), "was built
> for",
> platform), call. = FALSE)
> }
> }
> }
> else stop(paste("Package", sQuote(pkgname), "has not been
> installed
> properly\n",
> "See the Note in ?library"), call. = FALSE)
> }
> checkNoGenerics <- function(env, pkg) {
> nenv <- env
> ns <-
> .Internal(getRegisteredNamespace(as.name(libraryPkgName(pkg))))
> if (!is.null(ns))
> nenv <- asNamespace(ns)
> if (exists(".noGenerics", envir = nenv, inherits = FALSE))
> TRUE
> else {
> length(objects(env, pattern = "^\\.__M", all = TRUE)) ==
> 0
> }
> }
> checkConflicts <- function(package, pkgname, pkgpath, nogenerics) {
> dont.mind <- c("last.dump", "last.warning", ".Last.value",
> ".Random.seed", ".First.lib", ".Last.lib", ".packageName",
> ".noGenerics", ".required")
> sp <- search()
> lib.pos <- match(pkgname, sp)
> ob <- objects(lib.pos, all = TRUE)
> if (!nogenerics && .isMethodsDispatchOn()) {
> these <- objects(lib.pos, all = TRUE)
> these <- these[substr(these, 1, 6) == ".__M__"]
> gen <- gsub(".__M__(.*):([^:]+)", "\\1", these)
> from <- gsub(".__M__(.*):([^:]+)", "\\2", these)
> gen <- gen[from != ".GlobalEnv"]
> ob <- ob[!(ob %in% gen)]
> }
> fst <- TRUE
> ipos <- seq(along = sp)[-c(lib.pos, match("Autoloads",
> sp))]
> for (i in ipos) {
> obj.same <- match(objects(i, all = TRUE), ob, nomatch = 0)
> if (any(obj.same > 0)) {
> same <- ob[obj.same]
> same <- same[!(same %in% dont.mind)]
> Classobjs <- grep("^\\.__", same)
> if (length(Classobjs))
> same <- same[-Classobjs]
> if (length(same)) {
> if (fst) {
> fst <- FALSE
> cat("\nAttaching package ", sQuote(package),
> ":\n\n", sep = "")
> }
> cat("\n\tThe following object(s) are masked",
> if (i < lib.pos)
> "_by_"
> else "from", sp[i], ":\n\n\t", same, "\n\n")
> }
> }
> }
> }
> libraryPkgName <- function(pkgName, sep = "_")
> unlist(strsplit(pkgName,
> sep, fixed = TRUE))[1]
> libraryPkgVersion <- function(pkgName, sep = "_") {
> splitName <- unlist(strsplit(pkgName, sep, fixed = TRUE))
> if (length(splitName) > 1)
> splitName[2]
> else NULL
> }
> libraryMaxVersPos <- function(vers) {
> if (length(vers) == 0)
> return(integer(0))
> vers <- package_version(vers)
> max <- vers[1]
> for (i in seq(along = vers)) if (max < vers[i])
> max <- vers[i]
> which(vers == max)[1]
> }
> runUserHook <- function(pkgname, pkgpath) {
> hook <- getHook(packageEvent(pkgname, "attach"))
> for (fun in hook) try(fun(pkgname, pkgpath))
> }
> if (!missing(package)) {
> if (is.null(lib.loc))
> lib.loc <- .libPaths()
> if (!character.only)
> package <- as.character(substitute(package))
> if (package %in% c("ctest", "eda", "modreg", "mva", "nls",
> "stepfun", "ts")) {
> have.stats <- "package:stats" %in% search()
> if (!have.stats)
> require("stats")
> warning("package ", sQuote(package), " has been merged
> into ",
> sQuote("stats"), call. = FALSE)
> return(if (logical.return) TRUE else
> invisible(.packages()))
> }
> if (package == "mle") {
> have.stats4 <- "package:stats4" %in% search()
> if (!have.stats4)
> require("stats4")
> warning("package ", sQuote(package), " has been merged
> into ",
> sQuote("stats4"), call. = FALSE)
> return(if (logical.return) TRUE else
> invisible(.packages()))
> }
> if (package == "lqs") {
> cat("Package", sQuote("lqs"), "has been moved back to
> package",
> sQuote("MASS"), "\n")
> have.VR <- "package:MASS" %in% search()
> if (!have.VR) {
> if (require("MASS", quietly = TRUE))
> cat("Package", sQuote("MASS"), "has now been
> loaded\n")
> else {
> if (logical.return)
> return(FALSE)
> else stop(paste("Package", sQuote("MASS"),
> "seems to be missing", "from this R installation"))
> }
> }
> return(if (logical.return) TRUE else
> invisible(.packages()))
> }
> if (!missing(version)) {
> package <- manglePackageName(package, version)
> }
> else {
> pkgDirs <- list.files(lib.loc, pattern = paste("^",
> package, sep = ""))
> if (length(pkgDirs) > 0) {
> if (!(package %in% pkgDirs)) {
> vers <- unlist(lapply(pkgDirs, libraryPkgVersion))
> vpos <- libraryMaxVersPos(vers)
> if (length(vpos) > 0)
> package <- pkgDirs[vpos]
> }
> }
> }
> if (length(package) != 1)
> stop(paste("argument", sQuote("package"), "must be of
> length
> 1"))
> pkgname <- paste("package", package, sep = ":")
> newpackage <- is.na(match(pkgname, search()))
> if (newpackage) {
> pkgpath <- .find.package(package, lib.loc, quiet = TRUE,
> verbose = verbose)
> if (length(pkgpath) == 0) {
> txt <- paste("There is no package called",
> sQuote(libraryPkgName(package)))
> vers <- libraryPkgVersion(package)
> if (!is.null(vers))
> txt <- paste(txt, ", version ", vers, sep = "")
> if (logical.return) {
> warning(txt)
> return(FALSE)
> }
> else stop(txt)
> }
> which.lib.loc <- dirname(pkgpath)
> pfile <- system.file("Meta", "package.rds", package =
> package,
> lib.loc = which.lib.loc)
> if (!nchar(pfile))
> stop(sQuote(libraryPkgName(package)), " is not a valid
> package -- installed < 2.0.0?")
> pkgInfo <- .readRDS(pfile)
> testRversion(pkgInfo, package)
> if (is.character(pos)) {
> npos <- match(pos, search())
> if (is.na(npos)) {
> warning(paste(sQuote(pos), "not found on search path,
> using",
> sQuote("pos=2")))
> pos <- 2
> }
> else pos <- npos
> }
> .getRequiredPackages2(pkgInfo)
> if (packageHasNamespace(package, which.lib.loc)) {
> tt <- try({
> ns <- loadNamespace(package, c(which.lib.loc,
> lib.loc))
> dataPath <- file.path(which.lib.loc, package,
> "data")
> env <- attachNamespace(ns, pos = pos, dataPath =
> dataPath)
> })
> if (inherits(tt, "try-error"))
> if (logical.return)
> return(FALSE)
> else stop("package/namespace load failed for ",
> sQuote(libraryPkgName(package)))
> else {
> on.exit(do.call("detach", list(name = pkgname)))
> nogenerics <- checkNoGenerics(env, package)
> if (warn.conflicts && !exists(".conflicts.OK",
> envir = env, inherits = FALSE))
> checkConflicts(package, pkgname, pkgpath,
> nogenerics)
> if (!nogenerics && .isMethodsDispatchOn() &&
> !identical(pkgname, "package:methods"))
> methods::cacheMetaData(env, TRUE, searchWhere =
> .GlobalEnv)
> runUserHook(package, pkgpath)
> on.exit()
> if (logical.return)
> return(TRUE)
> else return(invisible(.packages()))
> }
> }
> codeFile <- file.path(which.lib.loc, package, "R",
> libraryPkgName(package))
> loadenv <- new.env(hash = TRUE, parent = .GlobalEnv)
> assign(".packageName", package, envir = loadenv)
> if (file.exists(codeFile)) {
> res <- try(sys.source(codeFile, loadenv, keep.source =
> keep.source))
> if (inherits(res, "try-error"))
> stop("Unable to load R code in package ",
> sQuote(libraryPkgName(package)),
> call. = FALSE)
> }
> else if (verbose)
> warning(paste("Package ",
> sQuote(libraryPkgName(package)),
> "contains no R code"))
> dbbase <- file.path(which.lib.loc, package, "data",
> "Rdata")
> if (file.exists(paste(dbbase, ".rdb", sep = "")))
> lazyLoad(dbbase, loadenv)
> dbbase <- file.path(which.lib.loc, package, "R",
> "sysdata")
> if (file.exists(paste(dbbase, ".rdb", sep = "")))
> lazyLoad(dbbase, loadenv)
> env <- attach(NULL, pos = pos, name = pkgname)
> on.exit(do.call("detach", list(name = pkgname)))
> attr(env, "path") <- file.path(which.lib.loc, package)
> .Internal(lib.fixup(loadenv, env))
> if (exists(".First.lib", mode = "function", envir = env,
> inherits = FALSE)) {
> firstlib <- get(".First.lib", mode = "function",
> envir = env, inherits = FALSE)
> tt <- try(firstlib(which.lib.loc, package))
> if (inherits(tt, "try-error"))
> if (logical.return)
> return(FALSE)
> else stop(".First.lib failed for ",
> sQuote(libraryPkgName(package)))
> }
> if (!is.null(firstlib <-
> getOption(".First.lib")[[package]])) {
> tt <- try(firstlib(which.lib.loc, package))
> if (inherits(tt, "try-error"))
> if (logical.return)
> return(FALSE)
> else stop(".First.lib failed",
> sQuote(libraryPkgName(package)))
> }
> nogenerics <- checkNoGenerics(env, package)
> if (warn.conflicts && !exists(".conflicts.OK", envir = env,
> inherits = FALSE))
> checkConflicts(package, pkgname, pkgpath, nogenerics)
> if (!nogenerics && .isMethodsDispatchOn() &&
> !identical(pkgname,
> "package:methods"))
> methods::cacheMetaData(env, TRUE, searchWhere =
> .GlobalEnv)
> runUserHook(package, pkgpath)
> on.exit()
> }
> if (verbose && !newpackage)
> warning(paste("Package", sQuote(libraryPkgName(package)),
> "already present in search()"))
> }
> else if (!missing(help)) {
> if (!character.only)
> help <- as.character(substitute(help))
> pkgName <- help[1]
> pkgPath <- .find.package(pkgName, lib.loc, verbose = verbose)
> docFiles <- c(file.path(pkgPath, "Meta", "package.rds"),
> file.path(pkgPath, "INDEX"))
> if (file.exists(vignetteIndexRDS <- file.path(pkgPath,
> "Meta", "vignette.rds")))
> docFiles <- c(docFiles, vignetteIndexRDS)
> pkgInfo <- vector(length = 4, mode = "list")
> pkgInfo[[1]] <- paste("\n\t\tInformation on Package",
> sQuote(pkgName))
> readDocFile <- function(f) {
> if (basename(f) %in% "package.rds") {
> txt <- .readRDS(f)$DESCRIPTION
> nm <- paste(names(txt), ":", sep = "")
> formatDL(nm, txt, indent = max(nchar(nm)) + 3)
> }
> else if (basename(f) %in% "vignette.rds") {
> txt <- .readRDS(f)
> if (is.data.frame(txt) && nrow(txt))
> cbind(basename(gsub("\\.[[:alpha:]]+$", "",
> txt$File)), paste(txt$Title,
> paste(rep.int("(source",
> NROW(txt)), ifelse(txt$PDF != "", ", pdf",
> ""), ")", sep = "")))
> else NULL
> }
> else readLines(f)
> }
> for (i in which(file.exists(docFiles))) pkgInfo[[i +
> 1]] <- readDocFile(docFiles[i])
> y <- list(name = pkgName, path = pkgPath, info = pkgInfo)
> class(y) <- "packageInfo"
> return(y)
> }
> else {
> if (is.null(lib.loc))
> lib.loc <- .libPaths()
> db <- matrix(character(0), nr = 0, nc = 3)
> nopkgs <- character(0)
> for (lib in lib.loc) {
> a <- .packages(all.available = TRUE, lib.loc = lib)
> for (i in sort(a)) {
> file <- system.file("Meta", "package.rds", package = i,
> lib.loc = lib)
> title <- if (file != "") {
> tmp <- .readRDS(file)
> if (is.list(tmp))
> tmp <- tmp$DESCRIPTION
> tmp["Title"]
> }
> else NA
> if (is.na(title))
> title <- " ** No title available (pre-2.0.0
> install?) **
> "
> db <- rbind(db, cbind(i, lib, title))
> }
> if (length(a) == 0)
> nopkgs <- c(nopkgs, lib)
> }
> colnames(db) <- c("Package", "LibPath", "Title")
> if ((length(nopkgs) > 0) && !missing(lib.loc)) {
> if (length(nopkgs) > 1)
> warning(paste("libraries", paste(sQuote(nopkgs),
> collapse = ", "), "contain no packages"))
> else warning(paste("library", paste(sQuote(nopkgs)),
> "contains no package"))
> }
> y <- list(header = NULL, results = db, footer = NULL)
> class(y) <- "libraryIQR"
> return(y)
> }
> if (logical.return)
> TRUE
> else invisible(.packages())
> }
> <environment: namespace:base>
>> library(affy)
> Loading required package: Biobase
>> openVignette()
> Error: couldn't find function "openVignette"
>>
>
> on Wed Nov 17 09:12:04 2004, "Michael Sean Kent, DVM, DACVIM
> (Oncology)" said:
>
>
> -----------------------------------------------------------------------
> | David M. Rocke, Professor Phone: (530) 752-0510 |
> | Division of Biostatistics (Medicine) and (530) 752-7368 |
> | Department of Applied Science (Engineering) |
> | Co-Director of IDAV FAX: (530) 752-8894 |
> | University of California, Davis E-mail: dmrocke at ucdavis.edu |
> | Davis, CA 95616-8553 www.cipic.ucdavis.edu/~dmrocke |
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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