[Rd] Patching "update.packages" to enable updating of only a user defined subset of packages

From: Tal Galili <tal.galili_at_gmail.com>
Date: Mon, 18 Apr 2011 09:51:04 +0300

Hello dear R developers,

I recently found out that it is not possible to limit update.packages() to update only a few packages at a time.

The patch offered simply adds a 'subset' parameter and the statement bounded within "if(!missing(subset))" to implement it. The code is pasted bellow (and also attached as an .r file).

Might this patch be considered valuable to be added to R?

(in the code bellow I called the function "update.packages.2" so to not mask the original update.packages)

With much respect,


update.packages.2 <-
function (lib.loc = NULL, repos = getOption("repos"), contriburl = contrib.url(repos,

    type), method, instlib = NULL, ask = TRUE, available = NULL,     oldPkgs = NULL, ..., checkBuilt = FALSE, type = getOption("pkgType"), subset)

    text.select <- function(old) {

        update <- NULL
        for (k in seq_len(nrow(old))) {
            cat(old[k, "Package"], ":\n", "Version", old[k, "Installed"],
                "installed in", old[k, "LibPath"], if (checkBuilt)
                  paste("built under R", old[k, "Built"]), "\n",
                "Version", old[k, "ReposVer"], "available at",
                simplifyRepos(old[k, "Repository"], type))
            answer <- substr(readline("Update (y/N/c)?  "), 1L,
            if (answer == "c" | answer == "C") {
                cat("cancelled by user\n")
            if (answer == "y" | answer == "Y")
                update <- rbind(update, old[k, ])


    if (is.null(lib.loc))

        lib.loc <- .libPaths()
    if (is.null(available))

        available <- available.packages(contriburl = contriburl,
            method = method)
    if (is.null(oldPkgs)) {
        oldPkgs <- old.packages(lib.loc = lib.loc, contriburl = contriburl,
            method = method, available = available, checkBuilt = checkBuilt)
        if (is.null(oldPkgs))

    else if (!(is.matrix(oldPkgs) && is.character(oldPkgs)))
        stop("invalid 'oldPkgs'; must be a result from old.packages()")
 if(!missing(subset)) # if the user uses 'subset'
if(mode(subset) != "character") stop("'subset' must be a character vector (with names of packages)")
 ss <- oldPkgs[,"Package"] %in% subset # are there any old packages that the user would have liked to update?
 if(!any(ss)) {
cat("There are no available new updates for the packages you have entered \n ")
} # if not - then we can end the function here  oldPkgs <- oldPkgs[ss,] # else - we can go on, but this time only use a subset of the oldPkgs.
 if(sum(ss)==1) oldPkgs <- t(oldPkgs) # in case there is only 1 package to update, make sure the object "oldPkgs" is of the correct form (6 columns instead of 1 vector)

    update <- if (is.character(ask) && ask == "graphics") {

        if (.Platform$OS.type == "windows" || .Platform$GUI ==
            "AQUA" || (capabilities("tcltk") && capabilities("X11"))) {
            k <- select.list(oldPkgs[, 1L], oldPkgs[, 1L], multiple = TRUE,
                title = "Packages to be updated", graphics = TRUE)
            oldPkgs[match(k, oldPkgs[, 1L]), , drop = FALSE]
        else text.select(oldPkgs)


    else if (isTRUE(ask))

    else oldPkgs
    if (length(update)) {

        if (is.null(instlib))
            instlib <- update[, "LibPath"]
        libs <- unique(instlib)
        for (l in libs) install.packages(update[instlib == l,
            "Package"], l, contriburl = contriburl, method = method,
            available = available, ..., type = type)


# Example:
# old.packages()
# update.packages.2(subset = "MASS")

Contact me: Tal.Galili_at_gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)

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