[Bioc-devel] Problem with getBioC()
Goeman, J.J. (MSTAT)
J.J.Goeman at lumc.nl
Tue May 24 18:33:00 CEST 2005
Hi Robert and Seth,
I was too quick in apologizing. I do still have the same problem, which now did not turn up in installing affy, but in installing genefilter. Running getBioC() a second time installed everything without problems. But then reinstalling R again and running getBioC() gave the same problems installing affy again. It puzzles me completely! Some traceback() information below.
> I am wondering if this is related to the locale settings (are you
> using a non-English locale?) and some of the recent changes in R to
> support other character sets. Which would explain why we have
> not seen
> it - since we don't use non-English settings (anyone else out
> there with
> non-English settings willing to give this a try).
I do not think that this is a problem, as I'm running an English version of Windows.
> You might also try and set options(error=recover), to see
> if that pops
> you into a debugger at some useful point (did you try traceback()?)
> Also, debug(install.packages), and then running this, would help to
> narrow down just what we are looking for.
Traceback gives:
> traceback()
9: sprintf(gettext("unable to move temp installation '%d' to '%s'"),
file.path(tmpDir, curPkg), instPath)
8: warning(sprintf(gettext("unable to move temp installation '%d' to '%s'"),
file.path(tmpDir, curPkg), instPath), domain = NA, call. = FALSE)
7: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers)
6: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
installWithVers = installWithVers, dependencies = dependencies)
5: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy",
"annotate", "Biobase", "Biostrings", "DynDoc", "edd", "gcrma",
"genefilter", "geneplotter", "hgu95av2", "limma", "makecdfenv",
"marray", "matchprobes", "multtest", "pamr", "reposTools", "ROC",
"siggenes", "sma", "statmod", "tkWidgets", "vsn", "widgetTools",
"xtable"), repos = c("http://www.bioconductor.org/packages/bioc/stable",
"http://www.bioconductor.org/packages/data/annotation/stable",
"http://www.bioconductor.org/packages/data/experiment/stable",
"http://www.bioconductor.org/packages/omegahat/stable", "http://www.bioconductor.org/packages/lindsey/stable",
"http://cran.fhcrc.org"), lib = "C:/PROGRA~1/R/rw2010/library",
dependencies = c("Depends", "Imports"))
4: do.call("install.packages", args)
3: biocinstall(lib = "C:/PROGRA~1/R/rw2010/library", groupName = "default",
dependencies = c("Depends", "Imports"))
2: do.call("biocinstall", args)
1: getBioC()
Setting options(error=recover) gives me a huge amount of output which I can't make heads or tails of. I've put it down below.
> Or another experiment - try just downloading the zip file, to the
> desktop and then loading it...
That solves the problem, as my previous email showed. But it does not show why it occurs.
Best,
Jelle
> options(error=recover)
> debug(install.packages)
> getBioC()
Running getBioC version 0.7 with R version 2.1.0
Running biocinstall version 1.0 with R version 2.1.0
debugging in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy",
"annotate", "Biobase", "Biostrings", "DynDoc", "edd", "gcrma",
"genefilter", "geneplotter", "hgu95av2", "limma", "makecdfenv",
"marray", "matchprobes", "multtest", "pamr", "reposTools", "ROC",
"siggenes", "sma", "statmod", "tkWidgets", "vsn", "widgetTools",
"xtable"), repos = c("http://www.bioconductor.org/packages/bioc/stable",
"http://www.bioconductor.org/packages/data/annotation/stable",
"http://www.bioconductor.org/packages/data/experiment/stable",
"http://www.bioconductor.org/packages/omegahat/stable", "http://www.bioconductor.org/packages/lindsey/stable",
"http://cran.fhcrc.org"), lib = "C:/PROGRA~1/R/rw2010/library",
dependencies = c("Depends", "Imports"))
debug: {
explode_bundles <- function(a) {
contains <- .find_bundles(a, FALSE)
extras <- unlist(lapply(names(contains), function(x) paste(contains[[x]],
" (", x, ")", sep = "")))
sort(as.vector(c(a[, 1], extras)))
}
if (missing(pkgs) || !length(pkgs)) {
if (.Platform$OS.type == "windows" || .Platform$GUI ==
"AQUA") {
if (is.null(available))
available <- available.packages(contriburl = contriburl,
method = method)
if (NROW(available)) {
a <- explode_bundles(available)
pkgs <- select.list(a, multiple = TRUE, title = "Packages")
}
if (!length(pkgs))
stop("no packages were specified")
}
else if (.Platform$OS.type == "unix" && capabilities("tcltk") &&
capabilities("X11")) {
if (is.null(available))
available <- available.packages(contriburl = contriburl,
method = method)
if (NROW(available)) {
a <- explode_bundles(available)
pkgs <- tcltk::tk_select.list(a, multiple = TRUE,
title = "Packages")
}
if (!length(pkgs))
stop("no packages were specified")
}
else stop("no packages were specified")
}
if (missing(lib) || is.null(lib)) {
lib <- .libPaths()[1]
if (length(.libPaths()) > 1)
warning(gettextf("argument 'lib' is missing: using %s",
lib), immediate. = TRUE, domain = NA)
}
if (.Platform$OS.type == "windows") {
if (type == "mac.binary")
stop("cannot install MacOS X binary packages on Windows")
if (type == "win.binary") {
.install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
installWithVers = installWithVers, dependencies = dependencies)
return(invisible())
}
}
else {
if (type == "mac.binary") {
if (!length(grep("darwin", R.version$platform)))
stop("cannot install MacOS X binary packages on this plaform")
.install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
installWithVers = installWithVers, dependencies = dependencies)
return(invisible())
}
if (type == "win.binary")
stop("cannot install Windows binary packages on this plaform")
if (!file.exists(file.path(R.home(), "bin", "INSTALL")))
stop("This version of R is not set up to install source packages\nIf it was installed from an RPM, you may need the R-devel RPM")
}
if (is.null(repos) & missing(contriburl)) {
update <- cbind(pkgs, lib)
cmd0 <- paste(file.path(R.home(), "bin", "R"), "CMD INSTALL")
if (installWithVers)
cmd0 <- paste(cmd0, "--with-package-versions")
for (i in 1:nrow(update)) {
cmd <- paste(cmd0, "-l", shQuote(update[i, 2]), shQuote(update[i,
1]))
if (system(cmd) > 0)
warning(gettextf("installation of package '%s' had non-zero exit status",
update[i, 1]), domain = NA)
}
return(invisible())
}
oneLib <- length(lib) == 1
tmpd <- destdir
nonlocalcran <- length(grep("^file:", contriburl)) < length(contriburl)
if (is.null(destdir) && nonlocalcran) {
tmpd <- file.path(tempdir(), "downloaded_packages")
if (!file.exists(tmpd) && !dir.create(tmpd))
stop(gettextf("Unable to create temporary directory '%s'",
tmpd), domain = NA)
}
depends <- is.character(dependencies) || (is.logical(dependencies) &&
dependencies)
if (depends && is.logical(dependencies))
dependencies <- c("Depends", "Imports", "Suggests")
if (depends && !oneLib) {
warning("Do not know which element of 'lib' to install dependencies into\nskipping dependencies")
depends <- FALSE
}
if (is.null(available))
available <- available.packages(contriburl = contriburl,
method = method)
bundles <- .find_bundles(available)
for (bundle in names(bundles)) pkgs[pkgs %in% bundles[[bundle]]] <- bundle
if (depends) {
p0 <- p1 <- unique(pkgs)
have <- .packages(all.available = TRUE)
repeat {
if (any(miss <- !p1 %in% row.names(available))) {
cat(sprintf(ngettext(sum(miss), "dependency %s is not available",
"dependencies %s are not available"), paste(sQuote(p1[miss]),
collapse = ", ")), "\n\n", sep = "")
flush.console()
}
p1 <- p1[!miss]
deps <- as.vector(available[p1, dependencies])
deps <- .clean_up_dependencies(deps, available)
if (!length(deps))
break
toadd <- deps[!deps %in% c("R", have, pkgs)]
if (length(toadd) == 0)
break
pkgs <- c(toadd, pkgs)
p1 <- toadd
}
for (bundle in names(bundles)) pkgs[pkgs %in% bundles[[bundle]]] <- bundle
pkgs <- unique(pkgs)
pkgs <- pkgs[pkgs %in% row.names(available)]
if (length(pkgs) > length(p0)) {
added <- setdiff(pkgs, p0)
cat(ngettext(length(added), "also installing the dependency ",
"also installing the dependencies "), paste(sQuote(added),
collapse = ", "), "\n\n", sep = "")
flush.console()
}
}
foundpkgs <- download.packages(pkgs, destdir = tmpd, available = available,
contriburl = contriburl, method = method, type = "source")
if (!is.null(foundpkgs)) {
update <- unique(cbind(pkgs, lib))
colnames(update) <- c("Package", "LibPath")
found <- pkgs %in% foundpkgs[, 1]
files <- foundpkgs[match(pkgs[found], foundpkgs[, 1]),
2]
update <- cbind(update[found, , drop = FALSE], file = files)
if (nrow(update) > 1) {
upkgs <- unique(pkgs <- update[, 1])
DL <- .make_dependency_list(upkgs, available)
p0 <- .find_install_order(upkgs, DL)
update <- update[sort.list(match(pkgs, p0)), ]
}
cmd0 <- paste(file.path(R.home(), "bin", "R"), "CMD INSTALL")
if (installWithVers)
cmd0 <- paste(cmd0, "--with-package-versions")
for (i in 1:nrow(update)) {
cmd <- paste(cmd0, "-l", shQuote(update[i, 2]), update[i,
3])
status <- system(cmd)
if (status > 0)
warning(gettextf("installation of package '%s' had non-zero exit status",
update[i, 1]), domain = NA)
}
if (!is.null(tmpd) && is.null(destdir))
cat("\n", gettextf("The downloaded packages are in\n\t%s",
normalizePath(tmpd)), "\n", sep = "")
link.html.help(verbose = TRUE)
}
else if (!is.null(tmpd) && is.null(destdir))
unlink(tmpd, TRUE)
invisible()
}
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