[Bioc-devel] Problem with getBioC()
Robert Gentleman
rgentlem at fhcrc.org
Tue May 24 19:01:34 CEST 2005
Hi,
Goeman, J.J. (MSTAT) wrote:
> 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()
so use options(error=recover)
select the frame for sprintf and then see what tmpDir, curPkg and
instPath are, one suspects that therein lies the problem
>
> 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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