Entering edit mode
David Rocke
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@david-rocke-1023
Last seen 10.2 years ago
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@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 <-
.InternalgetRegisteredNamespaceas.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,
pasterep.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@ucdavis.edu
|
| Davis, CA 95616-8553 www.cipic.ucdavis.edu/~dmrocke
|
