James - that worked perfectly.  Many thanks.

Dr David Iles
Visiting Research Fellow
School of Biology
University of Leeds
Leeds LS2 9JT

From: James Eales <jeales@gmail.com<mailto:jeales@gmail.com>>
Date: Wednesday, 16 April 2014 11:08
To: "r-sig-mac@googlegroups.com<mailto:r-sig-mac@googlegroups.com>" <r-sig-mac@googlegroups.com<mailto:r-sig-mac@googlegroups.com>>
Cc: "R-SIG-Mac@R-project.org<mailto:R-SIG-Mac@R-project.org>" <R-SIG-Mac@r-project.org<mailto:R-SIG-Mac@r-project.org>>, Dave Iles <daveiles@omicsltd.com<mailto:daveiles@omicsltd.com>>
Subject: Re: [R-SIG-Mac] OS X R console Package Manager error

Hello,
I had exactly the same trouble
Try pasting this into the console then click "Package Manager" again

package.manager <- function ()
{
    if (.Platform$GUI != "AQUA")
        stop("this function is intended to work with the Aqua GUI")
    loaded.pkgs <- .packages()
    x <- library()
    x <- x$results[x$results[, 1] != "base", ]
    pkgs <- x[, 1]
    pkgs.desc <- x[, 3]
    is.loaded <- !is.na<http://is.na/>(match(pkgs, loaded.pkgs))
    pkgs.status <- character(length(is.loaded))
    pkgs.status[which(is.loaded)] <- "loaded"
    pkgs.status[which(!is.loaded)] <- " "
    pkgs.url <- file.path(find.package(pkgs), "html", "00Index.html")
    load.idx <- .Call("pkgmanager", is.loaded, pkgs, pkgs.desc,
        pkgs.url)
    toload <- which(load.idx & !is.loaded)
    tounload <- which(is.loaded & !load.idx)
    for (i in tounload) {
        cat("unloading package:", pkgs[i], "\n")
        do.call("detach", list(paste("package", pkgs[i], sep = ":")))
    }
    for (i in toload) {
        cat("loading package:", pkgs[i], "\n")
        library(pkgs[i], character.only = TRUE)
    }
}

On Wednesday, 16 April 2014 10:20:49 UTC+1, David Iles wrote:
Hi Folks,

I updated my version of R yesterday using the R-3.1.0-snowleopard.pkg downloaded from CRAN. I tried to open Package Manager, but it failed to open, with the following message....

Error: '.find.package' is defunct.
Use 'find.package' instead.
See help("Defunct")

I deleted R.app and the R frameworks folder, and re-installed R from scratch, but the error persists. Clearly I have missed something from previous installations that is still lurking somewhere on my computer. Can anyone point me to what I need to delete/edit/update to correct this issue?

Many thanks,

Dr David Iles
Visiting Research Fellow
School of Biology
University of Leeds
Leeds LS2 9JT

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
>

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