[BioC] Installation Problem on OS X

David Rocke dmrocke at ucdavis.edu
Tue Nov 23 19:27:28 CET 2004


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 |



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