R/valid.R

In BiocManager: Access the Bioconductor Project Package Repository

.valid_pkgs_too_new <-
    function(instPkgs, availPkgs)
{
    idx <- rownames(availPkgs) %in% rownames(instPkgs)
    vers <- availPkgs[idx, "Version"]
    idx <- package_version(vers) <
        package_version(instPkgs[names(vers), "Version"])
    too_new <- names(vers)[idx]
    instPkgs[too_new, c("Version", "LibPath"), drop=FALSE]
}

.valid_out_of_date_pkgs <-
    function(pkgs = installed.packages(lib.loc, priority=priority), repos,
             lib.loc=NULL, priority="NA", type=getOption("pkgType"),
             filters=NULL, ..., checkBuilt, site_repository)
{
    contribUrl <- contrib.url(repos, type=type)

    available <- out_of_date <- too_new <- character()
    result <- FALSE
    available <- .inet_available.packages(
        contribUrl, type=type, filters=filters
    )
    out_of_date <- .inet_old.packages(
        lib.loc, repos=repos, instPkgs=pkgs,
        available=available, checkBuilt=checkBuilt, type=type
    )
    list(
        available = available,
        out_of_date = out_of_date,
        noRepos = !length(repos)
    )
}

.valid_out_of_date_filter <- function(out_of_date) {
    out_of_date[rownames(out_of_date) != "BiocVersion", , drop = FALSE]
}

.valid_result <-
    function(avail_out, pkgs = installed.packages(lib.loc, priority=priority),
             lib.loc=NULL, priority="NA")
{
    too_new <- .valid_pkgs_too_new(pkgs, avail_out[["available"]])
    out_of_date <- .valid_out_of_date_filter(avail_out[["out_of_date"]])

    result <- !nrow(too_new) && (is.null(out_of_date) || !nrow(out_of_date))

    if (!result || avail_out[["noRepos"]]) {
        result <- structure(
            list(out_of_date = out_of_date, too_new = too_new),
            class="biocValid"
        )
    }
    result
}

#' Validate installed package versions against correct versions.
#'
#' Check that installed packages are consistent (neither out-of-date
#' nor too new) with the version of R and _Bioconductor_ in use.
#'
#' @details This function compares the version of installed packages
#'   to the version of packages associated with the version of _R_
#'   and _Bioconductor_ currently in use.
#'
#'   Packages are reported as 'out-of-date' if a more recent version
#'   is available at the repositories specified by
#'   `BiocManager::repositories()`.  Usually, `BiocManager::install()` is
#'   sufficient to update packages to their most recent version.
#'
#'   Packages are reported as 'too new' if the installed version is
#'   more recent than the most recent available in the
#'   `BiocManager::repositories()`. It is possible to down-grade by
#'   re-installing a too new package "PkgA" with
#'   `BiocManger::install("PkgA")`. It is important for the user to
#'   understand how their installation became too new, and to avoid
#'   this in the future.
#'
#' @param pkgs A character() vector of package names for checking, or
#'     a matrix as returned by \code{\link{installed.packages}()}`.
#' @param lib.loc A character() vector of library location(s) of
#'     packages to be validated; see \code{\link{installed.packages}()}.
#' @param priority character(1) Check validity of all, "base", or
#'     "recommended" packages; see \code{\link{installed.packages}()}.
#' @param type character(1) The type of available package (e.g.,
#'     binary, source) to check validity against; see
#'     \code{\link{available.packages}()}.
#' @param filters character(1) Filter available packages to check
#'     validity against; see \code{\link{available.packages}()}.
#' @param \dots Additional arguments, passed to
#'     \code{BiocManager::\link{install}()} when `fix=TRUE`.
#' @param checkBuilt `logical(1)`. If `TRUE` a package built under an
#'     earlier major.minor version of R (e.g., 3.4) is considered to
#'     be old.
#' @param site_repository `character(1)`. See `?install`.
#' @return `biocValid` list object with elements `too_new` and
#'     `out_of_date` containing `data.frame`s with packages and their
#'     installed locations that are too new or out-of-date for the
#'     current version of _Bioconductor_. When internet access
#'     is unavailable, an empty 'biocValid' list is returned. If all
#'     packages ('pkgs') are up to date, then TRUE is returned.
#' @author Martin Morgan \email{martin.morgan@@roswellpark.org}
#' @seealso \code{BiocManager::\link{install}()} to update installed
#'     packages.
#' @keywords environment
#' @examples
#' if (interactive()) {
#'   BiocManager::valid()
#' }
#' @md
#' @export valid
valid <-
    function(pkgs = installed.packages(lib.loc, priority=priority),
             lib.loc=NULL, priority="NA", type=getOption("pkgType"),
             filters=NULL, ..., checkBuilt = FALSE,
             site_repository = character())
{
    stopifnot(
        is.logical(checkBuilt), length(checkBuilt) == 1L, !is.na(checkBuilt)
    )
    site_repository <- .repositories_site_repository(site_repository)

    if (!is.matrix(pkgs)) {
        if (is.character(pkgs)) {
            pkgs <- installed.packages(pkgs, lib.loc=lib.loc)
        } else {
            .stop(
                "'pkgs' must be a character vector of package names,
                 or a matrix like that returned by 'installed.packages()'"
            )
        }
    }
    version <- .version_validate(version())
    repos <- .repositories(site_repository, version = version)
    repos <- .repositories_filter(repos)

    vout <- .valid_out_of_date_pkgs(pkgs = pkgs, lib.loc = lib.loc,
        repos = repos, priority = priority, type = type, filters=filters, ...,
        checkBuilt = checkBuilt, site_repository = site_repository)

    result <-
        .valid_result(vout, pkgs = pkgs, lib.loc = lib.loc, priority = priority)

    if (!isTRUE(result)) {
        out_of_date <- result$out_of_date
        too_new <- result$too_new
        if (NROW(out_of_date) + NROW(too_new) != 0L) {
            .warning(
                "%d packages out-of-date; %d packages too new",
                NROW(out_of_date), NROW(too_new)
            )
        }
    }
    result
}

#' @rdname valid
#' @param x A `biocValid` object returned by `BiocManager::valid()`.
#' @return `print()` is invoked for its side effect.
#' @export
print.biocValid <-
    function(x, ...)
{
    cat("\n* sessionInfo()\n\n")
    print(sessionInfo())

    cat(
        "\nBioconductor version '", as.character(version()), "'",
        "\n",
        "\n  * ", NROW(x$out_of_date), " packages out-of-date",
        "\n  * ", NROW(x$too_new), " packages too new",
        sep = ""
    )

    n <- NROW(x$too_new) + NROW(x$out_of_date)
    if (n == 0L) {
        cat("\n\nInstallation valid\n")
        return()
    }

    fmt <-'  BiocManager::install(%s, update = TRUE, ask = FALSE, force = TRUE)'
    if (n == 1L) {
        fmt <- sprintf(fmt, '"%s"')
    } else {
        fmt <- sprintf(fmt, 'c(\n    "%s"\n  )')
    }

    pkgs0 <- sort(unique(c(rownames(x$too_new), rownames(x$out_of_date))))
    pkgs <- paste(strwrap(
        paste(pkgs0, collapse='", "'),
        width = getOption("width") - 4L
    ), collapse="\n    ")
    cat(
        "\n\ncreate a valid installation with",
        "\n\n", sprintf(fmt, pkgs), "\n\n",
        sep = ""
    )
    cat("more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date\n\n")
}