#  File src/library/utils/R/packages.R
#  Part of the R package, https://www.R-project.org
#
#  Copyright (C) 1995-2025 The R Core Team
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  A copy of the GNU General Public License is available at
#  https://www.R-project.org/Licenses/

available.packages <-
function(contriburl = contrib.url(repos, type), method,
         fields = getOption("available_packages_fields"),
         type = getOption("pkgType"), filters = NULL,
         repos = getOption("repos"),
         ignore_repo_cache = FALSE, max_repo_cache_age,
         cache_user_dir = str2logical(Sys.getenv("R_PACKAGES_CACHE_USER_DIR", FALSE)),
         quiet = TRUE, verbose = FALSE, ...)
{
    if (!is.character(type))
        stop(gettextf("'%s' must be a character string", "type"), domain = NA)
    ## We need Built if any of the URLs are binaries. At this point we don't enforce that url/type
    ## match, partially because we don't actually use that information, but in case we are
    ## on a system with binaries the default pkgType will contain "binary" or "both" so we take it
    ## as a hint that one of them may be binary and thus we need "Built"
    requiredFields <-
        c(tools:::.get_standard_repository_db_fields(), "File", "Published",
          if(any(grepl("(binary|both)", type))) "Built")
    if (is.null(fields))
	fields <- requiredFields
    else {
	stopifnot(is.character(fields))
	fields <- unique(c(requiredFields, fields))
    }

    if(missing(max_repo_cache_age))
       max_repo_cache_age <- as.numeric(Sys.getenv("R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE", "3600"))

    timestamp <- Sys.time()

    res <- matrix(NA_character_, 0L, length(fields) + 1L,
		  dimnames = list(NULL, c(fields, "Repository")))

    url_to_cache_name <- function(url)
    {
          # from rfc 3986
          re <- "^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"
          p <- unlist(regmatches(url, regexec(re, url)))[c(2,4,6,7,9)]
          names(p) <- c("scheme", "authority", "path", "query", "fragment")

          if (grepl("@", p["authority"], fixed=TRUE)) {
              rea <- "//([^@]*)@(.*)"
              pa <- unlist(regmatches(p["authority"],
                                      regexec(rea, p["authority"])))[c(2,3)]
              names(pa) <- c("userinfo", "hostport")
              if (nzchar(pa["userinfo"])) {
                  # replace user info by a hash
                  sha <- tools::sha256sum(bytes=charToRaw(pa["userinfo"]))
                  url <- paste0(p["scheme"], "//",
                                substr(sha, 49, 64), "@", pa["hostport"],
                                p["path"], p["query"], p["fragment"])
              }
          }
          URLencode(url, TRUE)
    }

    for(repos in unique(contriburl)) {
        localcran <- startsWith(repos, "file:")
        if(localcran) {
            ## see note in download.packages
            if(startsWith(repos, "file:///")) {
                tmpf <- paste0(substring(repos, 8L), "/PACKAGES")
                if(.Platform$OS.type == "windows") {
                    if(length(grep("^/[A-Za-z]:", tmpf)))
                        tmpf <- substring(tmpf, 2L)
                }
            } else {
                tmpf <- paste0(substring(repos, 6L), "/PACKAGES")
            }
            res0 <- if(file.exists(dest <- paste0(tmpf, ".rds")))
                readRDS(dest)
            else
                read.dcf(file = tmpf)
            if(length(res0))
                rownames(res0) <- res0[, "Package"]
        } else {
            used_dest <- FALSE
            if(ignore_repo_cache) {
                dest <- tempfile()
            } else {
                dest <- file.path(if(cache_user_dir) tools::R_user_dir("base", "cache")
                                  else tempdir(),
                                  paste0("repos_", url_to_cache_name(repos),
                                         ".rds"))
                if(file.exists(dest)) {
                    age <- difftime(timestamp, file.mtime(dest), units = "secs")
                    if(isTRUE(age < max_repo_cache_age)) {
                        res0 <- readRDS(dest)
                        used_dest <- TRUE
                        ## Be defensive :
                        if(length(res0))
                            rownames(res0) <- res0[, "Package"]
                    }
                    else
                        unlink(dest)    # Cache too old.
                }
            }
            if(!used_dest) {
                ## Try .rds and readRDS(), and then .gz or plain DCF and
                ## read.dcf(), catching problems from both missing or
                ## invalid files.
                need_dest <- FALSE
                op <- options(warn = -1L)
                z <- tryCatch({
                    z <- download.file(url = paste0(repos, "/PACKAGES.rds"),
                                       destfile = dest, method = method,
                                       cacheOK = FALSE, quiet = quiet,
                                       mode = "wb", ...)
                    if(z != 0L)
                        stop(gettextf("'download.file()' error code '%d'", z))
                }, error = identity)
                options(op)
                if(!inherits(z, "error")) {
                    z <- res0 <- tryCatch(readRDS(dest), error = identity)
                    if(ignore_repo_cache) unlink(dest)
                }

                if(inherits(z, "error")) {
                    ## Downloading or reading .rds failed, so try the
                    ## DCF variants.
                    if(!ignore_repo_cache) need_dest <- TRUE
                    tmpf <- tempfile()
                    on.exit(unlink(tmpf))
                    op <- options(warn = -1L)
                    ## FIXME: this should check the return value == 0L
                    z <- tryCatch({
                        ## This is a binary file
                        z <- download.file(url = paste0(repos, "/PACKAGES.gz"),
                                           destfile = tmpf, method = method,
                                           cacheOK = FALSE, quiet = quiet,
                                           mode = "wb", ...)
                        if(z != 0L)
                            stop(gettextf("'download.file()' error code '%d'", z))
                    }, error = identity)
                    if(inherits(z, "error"))
                        z <- tryCatch({
                            ## read.dcf is going to interpret CRLF as
                            ## LF, so use binary mode to avoid CRLF.
                            z <- download.file(url = paste0(repos, "/PACKAGES"),
                                          destfile = tmpf, method = method,
                                          cacheOK = FALSE, quiet = quiet,
                                          mode = "wb", ...)
                            if(z != 0L)
                                stop(gettextf("'download.file()' error code '%d'", z))
                        }, error = identity)
                    options(op)

                    if (!inherits(z, "error"))
                        z <- res0 <- tryCatch(read.dcf(file = tmpf),
                                              error = identity)

                    unlink(tmpf)
                    on.exit()
                }

                if(inherits(z, "error")) {
                    warning(gettextf("unable to access index for repository %s",
                                     repos),
                            ":\n  ", conditionMessage(z),
                            call. = FALSE, immediate. = TRUE, domain = NA)
                    ## Do not cache incorrect results. It can be a page
                    ## from a web proxy about inaccessible network.
                    unlink(dest)
                    next
                }

                if(length(res0)) {
                    rownames(res0) <- res0[, "Package"]
                    if(need_dest)
                        saveRDS(res0, dest, compress = TRUE)
                } else if(!need_dest) {
                    ## download.file() gave an empty .rds
                    ## Do not cache empty results.
                    unlink(dest)
                }
            } # end of download vs cached
        } # end of localcran vs online
        if (length(res0)) {
            missingFields <- fields[!(fields %in% colnames(res0))]
            if (length(missingFields)) {
                toadd <- matrix(NA_character_, nrow = nrow(res0),
                                ncol = length(missingFields),
                                dimnames = list(NULL, missingFields))
                res0 <- cbind(res0, toadd)
            }
            if ("Path" %in% colnames(res0)) {
                rp <- rep.int(repos, nrow(res0))
                path <- res0[, "Path"]
                rp[!is.na(path)] <- paste(repos, path[!is.na(path)], sep = "/")
            } else rp <- repos
            res0 <- cbind(res0[, fields, drop = FALSE], Repository = rp)
            res <- rbind(res, res0, deparse.level = 0L)
        }
        if(verbose) cat("added", NROW(res0), "packages, from repos", sQuote(repos),
                        "to a total of", NROW(res), "\n")
    } ## end  for(repos in *)

    if(!length(res)) return(res)

    if(is.null(filters)) {
        filters <- getOption("available_packages_filters")
        if(is.null(filters))
            filters <- available_packages_filters_default
    }
    if(is.list(filters)) {
        ## If filters is a list with an add = TRUE element, add the
        ## given filters to the default ones.
        if(isTRUE(filters$add)) {
            filters$add <- NULL
            filters <- c(available_packages_filters_default, filters)
        }
    }
    for(f in filters) {
        if(!length(res)) break
        if(is.character(f)) {
            ## Look up the filters db.
            ## Could be nice and allow abbrevs or ignore case.
            f <- available_packages_filters_db[[f[1L]]]
        }
        if(!is.function(f))
            stop("invalid 'filters' argument.")
        res <- f(res)
    }

    res
}

available_packages_filters_default <-
    c("R_version", "OS_type", "subarch", "duplicates")

available_packages_filters_db <- new.env(hash = FALSE) # small

available_packages_filters_db$R_version <-
function(db)
{
    ## Ignore packages which don't fit our version of R.
    depends <- db[, "Depends"]
    depends[is.na(depends)] <- ""
    ## Collect the (versioned) R depends entries.
    x <- lapply(strsplit(gsub("[[:space:]]", "", depends), ",",
                         fixed = TRUE),
                function(s) s[startsWith(s, "R(")])
    lens <- lengths(x)
    pos <- which(lens > 0L)
    if(!length(pos)) return(db)
    lens <- lens[pos]
    ## Unlist.
    x <- unlist(x)
    end <- 3L + (substring(x, 4L, 4L) == "=")
    ## Extract ops.
    ops <- substring(x, 3L, end)
    ## Split target versions according to ops.
    v_t <- split(substring(x, end + 1L, nchar(x) - 1L), ops)
    ## Current R version.
    v_c <- getRversion()
    ## Compare current to target grouped by op.
    res <- logical(length(x))
    for(op in names(v_t))
        res[ops == op] <- do.call(op, list(v_c, v_t[[op]]))
    ## And assemble test results according to the rows of db.
    pos <- pos[!vapply(split(res, rep.int(seq_along(lens), lens)), all,
                       NA)]
    if(length(pos))
        db <- db[-pos, , drop = FALSE]
    db
}

available_packages_filters_db$OS_type <-
function(db)
{
    ## Ignore packages that do not fit our OS.
    OS_type <- db[, "OS_type"]
    db[is.na(OS_type) | (OS_type == .Platform$OS.type), , drop = FALSE]
}

available_packages_filters_db$subarch <-
function(db)
{
    ## Ignore packages that do not fit our sub-architecture.
    ## Applies only to Mac and Windows binary repositories.
    current <- .Platform$r_arch
    if(!nzchar(current)) return(db)
    archs <- db[, "Archs"]
    if(all(is.na(archs))) return(db)
    OK <- unlist(lapply(archs, function(x) {
        if(is.na(x)) return(TRUE)
        this <- strsplit(x, "[[:space:]]*,[[:space:]]*")[[1L]]
        current %in% this
    }))
    db[OK, , drop = FALSE]
}

available_packages_filters_db$duplicates <-
function(db)
    tools:::.remove_stale_dups(db)

filter_packages_by_depends_predicates <-
function(db, predicate, recursive = TRUE)
{
    ## Could also add a 'which' argument to specify which dependencies
    ## are taken.

    ## Drop all packages for which any (recursive) dependency does not
    ## satisfy the given predicate (implemented as a function computing
    ## TRUE or FALSE for each rows of the package db).

    ## Somewhat tricky because there may be depends missing from the db,
    ## which are taken not to satisfy the predicate unless they are
    ## standard packages.

    ## Determine all depends missing from the db.
    db1 <- data.frame(Package = db[, "Package"],
                      stringsAsFactors = FALSE)
    fields <- c("Depends", "Imports", "LinkingTo")
    for(f in fields)
        db1[[f]] <-
            lapply(db[, f], tools:::.extract_dependency_package_names)
    all_packages <- unique(unlist(db1[fields], use.names = FALSE))
    bad_packages <-
        all_packages[is.na(match(all_packages, db1$Package))]
    ## Drop the standard packages from these.
    bad_packages <-
        setdiff(bad_packages,
                unlist(tools:::.get_standard_package_names()))

    ## Packages in the db which do not satisfy the predicate.
    ind <- !predicate(db)
    ## Now find the recursive reverse dependencies of these and the
    ## non-standard packages missing from the db.
    rdepends <-
        tools::package_dependencies(db1$Package[ind], db = db1,
                                    reverse = TRUE,
                                    recursive = recursive)
    rdepends <- unique(unlist(rdepends))
    ind[match(rdepends, db1$Package, nomatch = 0L)] <- TRUE

    ## And drop these from the db.
    db[!ind, , drop = FALSE]
}

available_packages_filters_db$`license/FOSS` <-
function(db) {
    predicate <- function(db)
        tools:::analyze_licenses(db[, "License"], db)$is_verified
    filter_packages_by_depends_predicates(db, predicate)
}

available_packages_filters_db$`license/restricts_use` <-
function(db) {
    predicate <- function(db) {
        ru <- tools:::analyze_licenses(db[, "License"], db)$restricts_use
        !is.na(ru) & !ru
    }
    filter_packages_by_depends_predicates(db, predicate)
}

available_packages_filters_db$CRAN <-
function(db)
{
    packages <- db[, "Package"]
    dups <- packages[duplicated(packages)]
    drop <- integer()
    CRAN <- getOption("repos")["CRAN"]
    ## do nothing if there is no CRAN repos on the list
    if(is.na(CRAN)) return(db)
    for(d in dups) {
        pos <- which(packages == d)
        ind <- !startsWith(db[pos, "Repository"], CRAN)
        if(!all(ind)) drop <- c(drop, pos[ind])
    }
    if(length(drop)) db[-drop, , drop = FALSE] else db
}


## unexported helper function
simplifyRepos <- function(repos, type)
{
    tail <- substring(contrib.url("---", type), 4L)
    ind <- regexpr(tail, repos, fixed=TRUE)
    ind <- ifelse(ind > 0L, ind-1L, nchar(repos, type="c"))
    substr(repos, 1L, ind)
}

update.packages <- 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"))
{
    if (!is.character(type))
        stop(gettextf("'%s' must be a character string", "type"), domain = NA)
    force(ask)  # just a check that it is valid before we start work
    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", .builtRver(old[k, "Built"])),
                "\n",
                "Version", old[k, "ReposVer"], "available at",
                simplifyRepos(old[k, "Repository"], type))
            cat("\n")
            answer <- askYesNo("Update?")
            if(is.na(answer)) {
                cat("cancelled by user\n")
                return(invisible())
            }
            if(isTRUE(answer))
                update <- rbind(update, old[k,])
        }
        update
    }

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


    if(type == "both" && (!missing(contriburl) || !is.null(available))) {
        stop("specifying 'contriburl' or 'available' requires a single type, not type = \"both\"")
    }
    if(is.null(available)) {
        available <- if (type == "both" && .Platform$pkgType != "source")
                         .available.both(repos, method, ...)
                     else
                         available.packages(contriburl = contriburl, method = method, ...)
        if (missing(repos)) repos <- getOption("repos") # May have changed
    }
    if(!is.matrix(oldPkgs) && is.character(oldPkgs)) {
    	subset <- oldPkgs
    	oldPkgs <- NULL
    } else
    	subset <- NULL

    if(is.null(oldPkgs)) {
        ## since 'available' is supplied, 'contriburl' and 'method' are unused
	oldPkgs <- old.packages(lib.loc = lib.loc,
				contriburl = contriburl, method = method,
				available = available, checkBuilt = checkBuilt)
	if (missing(repos)) repos <- getOption("repos") # May have changed
	## prune package versions which are invisible to require()
	if(!is.null(oldPkgs)) {
	    pkg <- 0L
	    while(pkg < nrow(oldPkgs)) {
		pkg <- pkg + 1L
		if(find.package(oldPkgs[pkg], lib.loc = lib.loc) !=
		   find.package(oldPkgs[pkg], lib.loc = oldPkgs[pkg,2])) {
		    warning(sprintf("package '%s' in library '%s' will not be updated",
				    oldPkgs[pkg], oldPkgs[pkg, 2]),
			    call. = FALSE, immediate. = TRUE)
		    oldPkgs <- oldPkgs[-pkg, , drop = FALSE]
		    pkg <- pkg - 1L
		}
	    }
	}
	if(is.null(oldPkgs))
	    return(invisible())
    } else if (!(is.matrix(oldPkgs) && is.character(oldPkgs)))
	stop("invalid 'oldPkgs'; must be a character vector or a result from old.packages()")

    if(!is.null(subset)) {
    	oldPkgs <- oldPkgs[ rownames(oldPkgs) %in% subset, ,drop=FALSE]
    	if (nrow(oldPkgs) == 0)
    	    return(invisible())
    }

    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)) text.select(oldPkgs)
    else oldPkgs


    if(length(update)) {
        if(is.null(instlib)) instlib <-  update[, "LibPath"]
        ## do this a library at a time, to handle dependencies correctly.
        libs <- unique(instlib)
        for(l in libs)
            if (type == 'both')
                install.packages(update[instlib == l , "Package"], l,
                                 repos = repos, method = method,
                                 ..., type = type)
            else
                install.packages(update[instlib == l , "Package"], l,
                                 contriburl = contriburl, method = method,
                                 available = available, ..., type = type)
    }
}

## (see also indices.R but it strips the time, sadly)
.builtDate <- function(built) { ## see also tools::.split_description, but return NA if something went wrong
    ## also allow structure from package.rds (just in case)
    bc <- if (is.list(built) && is.character(built$Date))
              built$Date
          else
              strsplit(built, "; ", fixed=TRUE)[[1]]
    ## Note that the timestamp should be always in UTC
    ## Some systems overwrite this field with invalid timestaps so ignore those
    if (length(bc) >= 3L)
        tryCatch(as.POSIXct(bc[3], "UTC"), error=function(e) NA)
    else
        NA
}

.builtRver <- function(built) ## convert full "Built" string to just R version (unless it is already)
    gsub("^R ([0-9.]+).*", "\\1", built)

## this is a wrapper of available.packages that handles the special case of type="both"
## by calling available.packages twice: once with "source" and once with "binary",
## combing the result. Given that the combination step is subject to specific choices,
## the logic in this wrapper is tailored for internal use in update.packages and old.packages.
.available.both <- function(repos, method, ...) {
    ## "both" gets complicated as we have to use available.packages twice
    fields <- c(tools:::.get_standard_repository_db_fields(), "File", "Built")
    av.src <- available.packages(contriburl = contrib.url(repos, "source"), method = method, fields = fields, ...)
    av.bin <- available.packages(contriburl = contrib.url(repos, "binary"), method = method, fields = fields, ...)
    ## we keep things simple in that we use source unless there is the same binary version
    ## so that we can get at the Built field. This is more simple than in install.packages
    ## since we only care about determining whether a package is new, but not which type is
    ## preferred - install.packages will sort that out.
    pkg.src <- row.names(av.src)
    pkg.bin <- row.names(av.bin)
    bin.ver <- av.bin[pkg.bin, "Version"]
    src.ver <- av.src[pkg.bin, "Version"]
    use.bin <- pkg.bin[as.numeric_version(bin.ver) >= as.numeric_version(src.ver)]
    use.bin <- use.bin[!is.na(use.bin)]
    use.src <- pkg.src[pkg.src %notin% use.bin]
    rbind(av.src[use.src,], av.bin[use.bin, ])
}

old.packages <- function(lib.loc = NULL, repos = getOption("repos"),
                         contriburl = contrib.url(repos, type),
                         instPkgs = installed.packages(lib.loc = lib.loc, ...),
                         method, available = NULL, checkBuilt = FALSE,
                         ..., type = getOption("pkgType"))
{
    if (!is.character(type))
        stop(gettextf("'%s' must be a character string", "type"), domain = NA)
    if(is.null(lib.loc))
        lib.loc <- .libPaths()
    if(!missing(instPkgs)) {
        ## actually we need rather more than this
        if(!is.matrix(instPkgs) || !is.character(instPkgs[, "Package"]))
            stop("ill-formed 'instPkgs' matrix")
    }
    if(NROW(instPkgs) == 0L) return(NULL)

    ## NB: type is ignored if either available or contriburl is specified.
    ## update.packages() raises an error in that case, but we can't really do that,
    ## becuase we get called with available internally
    available <- if(is.null(available)) {
                     if (type == "both" && .Platform$pkgType != "source")
                         .available.both(repos, method, ...)
                     else
                         available.packages(contriburl = contriburl, method = method, ...)
                 } else tools:::.remove_stale_dups(available)

    update <- NULL

    ## safely attempt to parse a (possibly incomplete) timestamp in UTC
    .ts <- function(x) if (isTRUE(!is.na(x))) as.POSIXlt(x, optional=TRUE, tz="UTC") else NA

    needs.install <- function(repo, inst)
        ## if the repo version is higher, then it's obvious
        ((package_version(repo["Version"]) > package_version(inst["Version"])) ||
         ## otherwise it depends - on equal versions we still need to install if published/built is higher
         (package_version(repo["Version"]) == package_version(inst["Version"]) &&
          (isTRUE(.builtDate(repo["Built"]) > .builtDate(inst["Built"])) || ## new re-built binary
           isTRUE(.ts(repo["Published"]) > .ts(inst["Published"]))          ## new "invalidated" due to dependency
          )
         ))

    currentR <- minorR <- getRversion()
    minorR[[c(1L, 3L)]] <- 0L # set patchlevel to 0
    for(k in 1L:nrow(instPkgs)) {
        if (instPkgs[k, "Priority"] %in% "base") next
        z <- match(instPkgs[k, "Package"], available[, "Package"])
        if(is.na(z)) next
        onRepos <- available[z, ]
        ## works OK if Built: is missing (which it should not be)
	if((!checkBuilt || package_version(.builtRver(instPkgs[k, "Built"])) >= minorR) &&
           !needs.install(onRepos, instPkgs[k,])) next
        deps <- onRepos["Depends"]
        if(!is.na(deps)) {
            Rdeps <- tools:::.split_dependencies(deps)[["R", exact=TRUE]]
            if(length(Rdeps) > 1L && !do.call(Rdeps$op, list(currentR, Rdeps$version)))
                next
        }
        update <- rbind(update,
                        c(instPkgs[k, c("Package", "LibPath", "Version", "Built")],
                          onRepos["Version"], onRepos["Repository"]))
    }
    if(!is.null(update))
        colnames(update) <- c("Package", "LibPath", "Installed", "Built",
                              "ReposVer", "Repository")
    rownames(update) <- update[, "Package"]
    ## finally, remove any duplicate rows
    update[!duplicated(update), , drop = FALSE]
}

new.packages <- function(lib.loc = NULL, repos = getOption("repos"),
                         contriburl = contrib.url(repos, type),
                         instPkgs = installed.packages(lib.loc = lib.loc, ...),
                         method, available = NULL, ask = FALSE,
                         ..., type = getOption("pkgType"))
{
    if (!is.character(type))
        stop(gettextf("'%s' must be a character string", "type"), domain = NA)
    ask  # just a check that it is valid before we start work
    if(type == "both" && (!missing(contriburl) || !is.null(available))) {
        stop("specifying 'contriburl' or 'available' requires a single type, not type = \"both\"")
    }
    if(is.null(lib.loc)) lib.loc <- .libPaths()
    if(!is.matrix(instPkgs))
        stop(gettextf("no installed packages for (invalid?) 'lib.loc=%s'",
                      lib.loc), domain = NA)
    ## NB: this implicitly uses type="source" even if type="both" - c.f. contrib.url()
    ##     but that's ok here as there should not be binary packages without sources
    if(is.null(available))
        available <- available.packages(contriburl = contriburl,
                                        method = method, ...)

    installed <- unique(instPkgs[, "Package"])

    poss <- sort(unique(available[ ,"Package"])) # sort in local locale
    res <- setdiff(poss, installed)

    update <- character()
    graphics <- FALSE
    if(is.character(ask) && ask == "graphics") {
        ask <- TRUE
        if(.Platform$OS.type == "windows" || .Platform$GUI == "AQUA"
           || (capabilities("tcltk") && capabilities("X11")))
            graphics <- TRUE
    }
    if(isTRUE(ask)) {
        if(length(res))
            update <- res[match(select.list(res, multiple = TRUE,
                                            title = "New packages to be installed",
                                            graphics = graphics)
                                , res)]
        else message("no new packages are available")
    }
    if(length(update)) {
        if(type == "both")
            install.packages(update, lib = lib.loc[1L], method = method,
                             type = type, ...)
        else
            install.packages(update, lib = lib.loc[1L], contriburl = contriburl,
                             method = method, available = available,
                             type = type, ...)
        # Now check if they were installed and update 'res'
        dirs <- list.files(lib.loc[1L])
        updated <- update[update %in% dirs]
        res <- res[!res %in% updated]
    }
    res
}

.instPkgFields <- function(fields) {
    ## to be used in installed.packages() and similar
    requiredFields <-
        c(tools:::.get_standard_repository_db_fields(), "Built", "Published")
    if (is.null(fields))
	fields <- requiredFields
    else {
	stopifnot(is.character(fields))
	fields <- unique(c(requiredFields, fields))
    }
    ## Don't retain 'Package' and 'LibPath' fields as these are used to
    ## record name and path of installed packages.
    fields[! fields %in% c("Package", "LibPath")]
}


## Read packages' Description and aggregate 'fields' into a character matrix
## NB: this does not handle encodings, so only suitable for ASCII-only fields.
.readPkgDesc <- function(lib, fields, pkgs = list.files(lib))
{
    ## to be used in installed.packages() and similar
    ## As from 2.13.0 only look at metadata.
    ret <- matrix(NA_character_, length(pkgs), 2L+length(fields))
    for(i in seq_along(pkgs)) {
        pkgpath <- file.path(lib, pkgs[i])
        if(file.access(pkgpath, 5L)) next
        if (file.exists(file <- file.path(pkgpath, "Meta", "package.rds"))) {
            ## this is vulnerable to installs going on in parallel
            md <- try(readRDS(file))
            if(inherits(md, "try-error")) next
            desc <- md$DESCRIPTION[fields]
            if (!length(desc)) {
                warning(gettextf("metadata of %s is corrupt", sQuote(pkgpath)),
                        domain = NA)
                next
            }
            ret[i, ] <- c(pkgs[i], lib, desc)
        }
    }
    ret[!is.na(ret[, 1L]), , drop = FALSE]
}

installed.packages <-
    function(lib.loc = NULL, priority = NULL, noCache = FALSE,
             cache_user_dir = str2logical(Sys.getenv("R_PACKAGES_CACHE_USER_DIR", FALSE)),
             fields = NULL, subarch = .Platform$r_arch, ...)
{
    if(is.null(lib.loc))
        lib.loc <- .libPaths()
    if(!is.null(priority)) {
        if(!is.character(priority))
            stop("'priority' must be character or NULL")
        if(any(b <- priority %in% "high"))
            priority <- c(priority[!b], "recommended","base")
    }

    fields <- .instPkgFields(fields)
    retval <- matrix(character(), 0L, 2L + length(fields))
    for(lib in lib.loc) {
        if(noCache) {
            ret0 <- .readPkgDesc(lib, fields)
            if(length(ret0)) retval <- rbind(retval, ret0, deparse.level = 0L)
        } else {
            ## Previously used URLencode for e.g. Windows paths with drives
            ## This version works for very long file names.
            base <- paste(c(lib, fields), collapse = ",")
            ## add length and 64-bit CRC in hex (in theory, seems
            ## it is actually 32-bit on some systems)
            enc <- sprintf("%d_%s", nchar(base), .Call(C_crc64, base))
            dest <- file.path(if(cache_user_dir) tools::R_user_dir("base", "cache")
                              else tempdir(),
                              paste0("libloc_", enc, ".rds"))
            test <- file.exists(dest) &&
                file.mtime(dest) > file.mtime(lib) &&
                (val <- readRDS(dest))$base == base
            if(isTRUE(as.vector(test)))
                ## use the cache file
                retval <- rbind(retval, val$value)
            else {
                ret0 <- .readPkgDesc(lib, fields)
                if(length(ret0)) {
                    retval <- rbind(retval, ret0, deparse.level = 0L)
                    ## save the cache file
                    dir.create(dirname(dest), recursive = TRUE,
                               showWarnings = FALSE)
                    saveRDS(list(base = base, value = ret0), dest)
                } else unlink(dest)
            }
        }
    }

    .fixupPkgMat(retval, fields, priority, subarch)
}

.fixupPkgMat <- function(mat, fields, priority, subarch=NULL)
{
    ## to be used in installed.packages() and similar
    colnames(mat) <- c("Package", "LibPath", fields)
    if (length(mat) && !is.null(priority)) {
	keep <- !is.na(pmatch(mat[,"Priority"], priority,
			      duplicates.ok = TRUE))
	mat <- mat[keep, , drop = FALSE]
    }
    if (length(mat) && !is.null(subarch) && nzchar(subarch)) {
        archs <- strsplit(mat[, "Archs"], ", ", fixed = TRUE)
        keep <- unlist(lapply(archs,
                              function(x) is.na(x[1L]) || subarch %in% x))
	mat <- mat[keep, , drop = FALSE]
    }
    if (length(mat)) mat <- mat[, colnames(mat) != "Archs", drop = FALSE]
    if (length(mat)) rownames(mat) <- mat[, "Package"]
    mat
}


remove.packages <- function(pkgs, lib)
{
    if(!length(pkgs)) return(invisible())
    base <- vapply(pkgs, isBasePkg, FALSE)
    if(any(base)) {
        (if(all(base)) stop else warning)(
            sprintf(ngettext(sum(base),
                                 "package %s is a base package, and cannot be removed",
                                 "packages %s are base packages, and cannot be removed"),
                        paste(sQuote(pkgs[base]), collapse = ", ")),
            domain = NA)
        pkgs <- pkgs[!base]
    }

    updateIndices <- function(lib) {
        ## This matches what install.packages() does
        if(lib == .Library && .Platform$OS.type == "unix") {
            message("Updating HTML index of packages in '.Library'")
            make.packages.html(.Library)
        }
    }

    if(missing(lib) || is.null(lib)) {
        lib <- .libPaths()[1L]
	message(sprintf(ngettext(length(pkgs),
                                 "Removing package from %s\n(as %s is unspecified)",
                                 "Removing packages from %s\n(as %s is unspecified)"),
                        sQuote(lib), sQuote("lib")), domain = NA)
    }

    paths <- find.package(pkgs, lib)
    if(length(paths)) {
        unlink(paths, TRUE)
        for(lib in unique(dirname(paths))) updateIndices(lib)
    }
    invisible()
}

.download.file.method <- function(method)
{
    if (missing(method))
	method <- getOption("download.file.method", default = "auto")
    match.arg(method, c("auto", "internal", "wininet",
                        "libcurl", "wget", "curl", "lynx"))
}

download.packages <- function(pkgs, destdir, available = NULL,
                              repos = getOption("repos"),
                              contriburl = contrib.url(repos, type),
                              method, type = getOption("pkgType"),
                              local = FALSE, ...)
{
    if (!is.character(type))
        stop(gettextf("'%s' must be a character string", "type"), domain = NA)
    nonlocalcran <- !all(startsWith(contriburl, "file:")) || local
    if(nonlocalcran && !dir.exists(destdir))
        stop("'destdir' is not a directory")

    type <- resolvePkgType(type)

    if(is.null(available))
        available <-
            available.packages(contriburl = contriburl, method = method, ...)

    if (.download.file.method(method) %in% c("auto", "libcurl"))
        bulkdown <- matrix(character(), 0L, 3L)
    else
        bulkdown <- NULL

    retval <- matrix(character(), 0L, 2L)
    for(p in unique(pkgs))
    {
        ok <- (available[,"Package"] == p)
        ok <- ok & !is.na(ok)
        if(!any(ok))
            warning(gettextf("no package %s at the repositories", sQuote(p)),
                    domain = NA, immediate. = TRUE)
        else {
            if(sum(ok) > 1L) { # have multiple copies
                vers <- package_version(available[ok, "Version"])
                keep <- vers == max(vers)
                keep[duplicated(keep)] <- FALSE
                ok[ok][!keep] <- FALSE
            }
            ## in Oct 2009 we introduced file names in PACKAGES files
            File <- available[ok, "File"]
            ## strip build name for ext detection
            type <- gsub("^([[:lower:]]+[.]binary)[.].*", "\\1", type)
            ## this is just a fall-back if there is no File: so hopefully
            ## no longer used
            fn <- paste0(p, "_", available[ok, "Version"],
                         switch(type,
                                "source" = ".tar.gz",
                                "mac.binary" = ".tgz",
                                "win.binary" = ".zip",
                                ".tar.xz")) ## for any other binaries, but they should use File:
            have_fn <- !is.na(File)
            fn[have_fn] <- File[have_fn]
            repos <- available[ok, "Repository"]
            if(startsWith(repos, "file:")) { # local repository
                ## This could be file: + file path or a file:/// URL.
                if(startsWith(repos, "file:///")) {
                    ## We need to derive the file name from the URL
                    ## This is tricky as so many forms have been allowed,
                    ## and indeed external methods may do even more.
                    fn <- paste(substring(repos, 8L), fn, sep = "/")
                    ## This leaves a path beginning with /
                    if(.Platform$OS.type == "windows") {
                        if(length(grep("^/[A-Za-z]:", fn)))
                            fn <- substring(fn, 2L)
                    }
                } else {
                    fn <- paste(substring(repos, 6L), fn, sep = "/")
                }
                if(file.exists(fn)) {
                    if(local) file.copy(fn, destdir)
                    retval <- rbind(retval, c(p, fn))
                }
                else
                    warning(gettextf("package %s does not exist on the local repository", sQuote(p)),
                            domain = NA, immediate. = TRUE)
            } else {
                url <- paste(repos, fn, sep = "/")
                destfile <- file.path(destdir, fn)

                if (is.null(bulkdown)) {
                    # serial download
                    res <- try(download.file(url, destfile, method, mode = "wb",
                                             ...))
                    if(!inherits(res, "try-error") && res == 0L)
                        retval <- rbind(retval, c(p, destfile))
                    else
                        warning(gettextf("download of package %s failed", sQuote(p)),
                                domain = NA, immediate. = TRUE)
                } else
                    bulkdown <- rbind(bulkdown, c(p, destfile, url))
            }
        }
    }

    if (!is.null(bulkdown) && nrow(bulkdown) > 0) {
        # bulk download using libcurl
        urls <- bulkdown[,3]
        destfiles <- bulkdown[,2]
        ps <- bulkdown[,1]

        res <- try(download.file(urls, destfiles, "libcurl", mode = "wb", ...))
        if(!inherits(res, "try-error") && res == 0L) {
            if (length(urls) > 1) {
                retvals <- attr(res, "retvals")
                for(i in seq_along(retvals)) {
                    if (retvals[i] == 0L)
                        retval <- rbind(retval, c(ps[i], destfiles[i]))
                    else
                        warning(gettextf("download of package %s failed",
                                sQuote(ps[i])), domain = NA, immediate. = TRUE)
                }
            } else
                retval <- rbind(retval, c(ps, destfiles))
        } else
            for(p in ps)
                warning(gettextf("download of package %s failed", sQuote(p)),
                        domain = NA, immediate. = TRUE)
    }

    retval
}

resolvePkgType <- function(type) {
    ## Not entirely clear this is optimal
    ## This was built on the assumption that binaries are always a subset, so
    ## using sources covers everything necssary. Not only is that not guaranteed,
    ## but binaries now may have additional information such as build timestamps.
    if(type == "both") type <- "source"
    else if(type == "binary") type <- .Platform$pkgType
    type
}

contrib.url <- function(repos, type = getOption("pkgType"))
{
    if (!is.character(type))
        stop(gettextf("'%s' must be a character string", "type"), domain = NA)
    type <- resolvePkgType(type)
    if(is.null(repos)) return(NULL)
    if(!length(repos)) return(character())
    if("@CRAN@" %in% repos && interactive()) {
        cat(gettext("--- Please select a CRAN mirror for use in this session ---"),
            "\n", sep = "")
        flush.console()
        chooseCRANmirror()
        m <- match("@CRAN@", repos)
        nm <- names(repos)
        repos[m] <- getOption("repos")["CRAN"]
        if(is.null(nm)) nm <- rep.int("", length(repos))
        nm[m] <- "CRAN"
        names(repos) <- nm
    }
    if("@CRAN@" %in% repos) stop("trying to use CRAN without setting a mirror")

    ver <- paste(R.version$major,
                 strsplit(R.version$minor, ".", fixed=TRUE)[[1L]][1L], sep = ".")
    .contrib.path <- function(type, ver) {
        ## <os>.binary[.<build>]  where build has to match [[:alnum:]_-]+
        m <- regexec("^([[:lower:]]+)[.]binary(|[.]([[:alnum:]_-]+))$", type)

        if (length(m) && length(m[[1]]) == 4) {  ## binary spec?
            m <- m[[1]]
            l <- attr(m, "match.length")
            os <- substr(type, m[2], m[2] + l[2] - 1L)
            ## for historical reasons mac/win have different directory names
            os <- switch(os, mac = "macosx", win = "windows", os)

            if (l[3] > 0) ## have build name ?
                paste("bin", os, substr(type, m[4], m[4] + l[4] - 1L), "contrib", ver, sep = "/")
            else
                paste("bin", os, "contrib", ver, sep = "/")
        } else if (isTRUE(type == "source"))
            "src/contrib"
        else
            stop("invalid 'type'")
    }

    paste(gsub("/$", "", repos), .contrib.path(type, ver), sep = "/")
}

.getMirrors <- function(url, local.file, all, local.only)
{
    m <- NULL
    if(!local.only) {
        ## Try to handle explicitly failure to connect to CRAN.
        f <- tempfile()
        on.exit(unlink(f))
        m <- tryCatch({
            m <- download.file(url, destfile = f, quiet = TRUE)
            if(m != 0L)
                stop(gettextf("'download.file()' error code '%d'", m))
            read.csv(f, as.is = TRUE, encoding = "UTF-8")
        }, error=function(err) {
            warning(gettextf("failed to download mirrors file (%s); using local file '%s'",
                             conditionMessage(err), local.file),
                    call.=FALSE, immediate.=TRUE)
            NULL
        })
    }
    if(is.null(m))
        m <- read.csv(local.file, as.is = TRUE, encoding = "UTF-8")
    if(!all) m <- m[as.logical(m$OK), ]
    m
}

getCRANmirrors <- function(all = FALSE, local.only = FALSE)
{
    .getMirrors("https://cran.r-project.org/CRAN_mirrors.csv",
                file.path(R.home("doc"), "CRAN_mirrors.csv"),
                all = all, local.only = local.only)
}

.chooseMirror <- function(m, label, graphics, ind)
{
    if(is.null(ind) && !interactive())
        stop("cannot choose a ", label, " mirror non-interactively")
    if (length(ind))
        res <- as.integer(ind)[1L]
    else {
    	isHTTPS <- (startsWith(m[, "URL"], "https") &
                    grepl("secure_mirror_from_master",
                          m[, "Comment"],
                          fixed = TRUE))
    	mHTTPS <- m[isHTTPS,]
    	mHTTP <- m[!isHTTPS,]
        httpsLabel <- paste("Secure", label, "mirrors")
        httpLabel <- paste("Other", label, "mirrors")
        m <- mHTTPS
        res <- menu(c(m[, 1L], "(other mirrors)"), graphics, httpsLabel)
        if (res > nrow(m)) {
            m <- mHTTP
            res <- menu(m[, 1L], graphics, httpLabel)
        }
    }
    if (res > 0L) {
        URL <- m[res, "URL"]
        names(URL) <- m[res, "Name"]
        sub("/$", "", URL[1L])
    } else character()
}

chooseCRANmirror <- function(graphics = getOption("menu.graphics"), ind = NULL,
                             local.only = FALSE)
{
    m <- getCRANmirrors(all = FALSE, local.only = local.only)
    url <- .chooseMirror(m, "CRAN", graphics, ind)
    if (length(url)) {
        repos <- getOption("repos")
        repos["CRAN"] <- url
        options(repos = repos)
    }
    invisible()
}

chooseBioCmirror <- function(graphics = getOption("menu.graphics"), ind = NULL,
                             local.only = FALSE)
{
    m <- .getMirrors("https://bioconductor.org/BioC_mirrors.csv",
                     file.path(R.home("doc"), "BioC_mirrors.csv"),
                     all = FALSE, local.only = local.only)
    url <- .chooseMirror(m, "BioC", graphics, ind)
    if (length(url))
        options(BioC_mirror = url)
    invisible()
}

setRepositories <-
    function(graphics = getOption("menu.graphics"), ind = NULL,
             addURLs = character(), name = NULL)
{
    if(is.null(name) && is.null(ind) && !interactive())
        stop("cannot set repositories non-interactively")
    a <- .get_repositories()
    pkgType <- getOption("pkgType")
    if (!is.character(pkgType))
        stop("invalid options(\"pkgType\"); must be a character string")
    if (pkgType == "both") pkgType <- "source" #.Platform$pkgType
    if (pkgType == "binary") pkgType <- .Platform$pkgType
    ## strip build names (until we need them and start recording them)
    pkgType <- gsub("^([[:lower:]]+[.]binary)[.].*", "\\1", pkgType)
    thisType <- a[[pkgType]]
    a <- a[thisType, 1L:3L]
    repos <- getOption("repos")
    ## Now look for CRAN and any others in getOptions("repos")
    if("CRAN" %in% row.names(a) && !is.na(CRAN <- repos["CRAN"]))
        a["CRAN", "URL"] <- CRAN
    ## Set as default any already in the option.
    a[(a[["URL"]] %in% repos), "default"] <- TRUE
    new <- !(repos %in% a[["URL"]])
    if(any(new)) {
        aa <- names(repos[new])
        if(is.null(aa)) aa <- rep.int("", length(repos[new]))
        aa[aa == ""] <- repos[new][aa == ""]
        newa <- data.frame(menu_name=aa, URL=repos[new], default=TRUE)
        row.names(newa) <- aa
        a <- rbind(a, newa, deparse.level = 0L)
    }

    default <- a[["default"]]

    res <- if (length(name)) {
        m <- match(tolower(name), tolower(row.names(a)))
        if (any(is.na(m)))
            stop("No matching repositories found for ",
                 paste(name[is.na(m)], collapse=', '))
        m
    } else if(length(ind)) as.integer(ind)
    else {
        title <- if(graphics) "Repositories" else gettext("--- Please select repositories for use in this session ---\n")
        match(select.list(a[, 1L], a[default, 1L], multiple = TRUE, title,
                           graphics = graphics), a[, 1L])
    }
    if(length(res) || length(addURLs)) {
        repos <- a[["URL"]]
        names(repos) <- row.names(a)
        repos <- c(repos[res], addURLs)
        options(repos = repos)
    }
}

findCRANmirror <- function(type = c("src", "web"))
{
    e <- paste0("R_CRAN_", toupper(type))
    Sys.getenv(e, tools:::.get_CRAN_repository_URL())
}


## used in some BioC packages and their support in tools.
compareVersion <- function(a, b)
{
    if(is.na(a)) return(-1L)
    if(is.na(b)) return(1L)
    ## The nest two could be skipped if(inherits(x), "numeric_version")
    ## but the saving would be small.
    a <- as.integer(strsplit(a, "[.-]")[[1L]])
    b <- as.integer(strsplit(b, "[.-]")[[1L]])
    ## This does not handle malformed inputs which will give an error.
    for(k in seq_along(a))
        if(k <= length(b)) {
            if(a[k] > b[k]) return(1) else if(a[k] < b[k]) return(-1L)
        } else return(1L)
    if(length(b) > length(a)) return(-1L) else return(0L)
}

## ------------- private functions --------------------

## .clean_up_dependencies <- function(x, available = NULL)
## {
##     ## x is a character vector of Depends / Suggests / Imports entries
##     ## returns a character vector of all the package dependencies mentioned
##     x <- x[!is.na(x)]
##     if(!length(x)) return(x)
##     x <- unlist(strsplit(x, ",", fixed = TRUE), use.names = FALSE)
##     unique(sub("^[[:space:]]*([[:alnum:].]+).*$", "\\1" , x))
## }

.clean_up_dependencies <- function(x)
    unique.default(tools:::.extract_dependency_package_names(x))

.clean_up_dependencies2 <- function(x, installed, available)
{
    ## x is a character vector of Depends / Suggests / Imports entries.
    ## Returns a list of length 2, a character vector of the names of
    ## all the package dependencies mentioned that are not already
    ## satisfied and one of those which cannot be satisfied (possibly
    ## of the form "pkg (>= ver)')

    .split_dependencies <- function(x) {
        .split2 <- function(x) {
            ## some have had space before ,
            x <- sub('[[:space:]]+$', '', x)
            x <- unique(sub("^[[:space:]]*(.*)", "\\1" , x))
            names(x) <- sub("^([[:alnum:].]+).*$", "\\1" , x)
            x <- x[names(x) != "R"]
	    x <- x[nzchar(x)]
            ## FIXME: a better way to handle duplicates.
            ## However, there should not be any, and if there are
            ## Depends: should be the first.
            x <- x[!duplicated(names(x))]
            lapply(x, tools:::.split_op_version)
        }
        ## given one of more concatenations of Depends/Imports/Suggests fields,
        ## return a named list of list(name, [op, version])
        if(!any(nzchar(x))) return(list())
        unlist(lapply(strsplit(x, ","), .split2), FALSE, FALSE)
    }
    x <- x[!is.na(x)]
    if(!length(x)) return(list(character(), character()))
    xx <- .split_dependencies(x)
    if(!length(xx)) return(list(character(), character()))
    ## Then check for those we already have installed
    pkgs <- installed[, "Package"]
    have <- vapply(xx, function(x) {
        if(length(x) == 3L) {
            if (! x[[1L]] %in% pkgs ) return(FALSE)
            if(x[[2L]] != ">=") return(TRUE)
            ## We may have the package installed more than once
            ## which we get will depend on the .libPaths() order,
            ## so for now just see if any installed version will do.
            current <- as.package_version(installed[pkgs == x[[1L]], "Version"])
            target <- as.package_version(x[[3L]])
            any(do.call(x$op, list(current, target)))
        } else x[[1L]] %in% pkgs
    }, NA)
    xx <- xx[!have]
    if(!length(xx)) return(list(character(), character()))
    ## now check if we can satisfy the missing dependencies
    pkgs <- row.names(available)
    canget <- miss <- character()
    for (i in seq_along(xx)) {
        x <- xx[[i]]
        if(length(x) == 3L) {
            if (! x[[1L]] %in% pkgs ) { miss <- c(miss, x[[1L]]); next }
            if(x[[2L]] != ">=") { canget <- c(canget, x[[1L]]); next }
            ## we may have the package available more than once
            ## install.packages() will find the highest version.
            current <- as.package_version(available[pkgs == x[[1L]], "Version"])
            target <- as.package_version(x[[3L]])
            res <- any(do.call(x$op, list(current, target)))
            if(res) canget <- c(canget, x[[1L]])
            else  miss <- c(miss, paste0(x[[1L]], " (>= ", x[[3L]], ")"))
        } else if(x[[1L]] %in% pkgs) canget <- c(canget, x[[1L]])
        else miss <- c(miss, x[[1L]])
    }
    list(canget, miss)
}

.make_dependency_list <-
    function(pkgs, available,
             dependencies = c("Depends", "Imports", "LinkingTo"),
             recursive = FALSE)
{
    ## given a character vector of packages,
    ## return a named list of character vectors of their dependencies.
    ## If recursive = TRUE, do this recursively.
    if(!length(pkgs)) return(NULL)
    if(is.null(available))
        stop(gettextf("%s must be supplied", sQuote("available")), domain = NA)
    info <- available[pkgs, dependencies, drop = FALSE]
    x <- vector("list", length(pkgs)); names(x) <- pkgs
    if(recursive) {
        known <- row.names(available)
        xx <- vector("list", length(known)); names(xx) <- known
        info2 <-  available[, dependencies, drop = FALSE]
        for (i in seq_along(known))
            xx[[i]] <- .clean_up_dependencies(info2[i, ])
        for (i in pkgs) {
            p <- xx[[i]]
            p <- p[p %in% known]; p1 <- p
            repeat {
                extra <- unlist(xx[p1])
                extra <- extra[extra != i]
                extra <- extra[extra %in% known]
                deps <- unique(c(p, extra))
                if (length(deps) <= length(p)) break
                p1 <- deps[!deps %in% p]
                p <- deps
            }
            x[[i]] <- p
        }
    } else {
        for (i in seq_along(pkgs)) x[[i]] <- .clean_up_dependencies(info[i, ])
    }
    x
}

.find_install_order <- function(pkgs, dependencyList)
{
    ## given a character vector of packages, find an install order
    ## which reflects their dependencies.
    DL <- dependencyList[pkgs]
    ## some of the packages may be already installed, but the
    ## dependencies apply to those being got from CRAN.
    DL <- lapply(DL, function(x) x[x %in% pkgs])
    lens <- lengths(DL)
    if(all(lens > 0L)) {
        warning("every package depends on at least one other")
        return(pkgs)
    }
    done <- names(DL[lens == 0L]); DL <- DL[lens > 0L]
    while(length(DL)) {
        OK <- vapply(DL, function(x) all(x %in% done), NA)
        if(!any(OK)) {
            warning(gettextf("packages %s are mutually dependent",
                             paste(sQuote(names(DL)), collapse = ", ")),
                    domain = NA)
            return(c(done,  names(DL)))
        }
        done <- c(done, names(DL[OK]))
        DL <- DL[!OK]
    }
    done
}

## moved from tools/R/utils.R as this is now called in utils::.onLoad
.get_repositories <- function()
{
    rfile <- Sys.getenv("R_REPOSITORIES", unset = NA_character_)
    ## "NULL" has a special meaning during .onLoad()
    if(is.na(rfile) || rfile == "NULL" || !file_test("-f", rfile)) {
        rfile <- file.path(Sys.getenv("HOME"), ".R", "repositories")
        if(!file_test("-f", rfile))
            rfile <- file.path(R.home("etc"), "repositories")
    }
    .read_repositories(rfile)
}

.read_repositories <- function(file)
{
    db <- read.delim(file, header = TRUE, comment.char = "#",
                     colClasses = c(rep.int("character", 3L),
                                    rep.int("logical", 4L))) # allow for win64.binary
    db[, "URL"] <- .expand_BioC_repository_URLs(db[, "URL"])
    db
}

.write_repositories <-
function(repos, file = stdout(), ...)
{
    ## Use .write_repositories(getOption("repos")) to write the current
    ## option to a file which can be re-used by other R processes.
    x <- list(...)
    n <- length(repos)
    h <- "menu_name\tURL\tdefault\tsource\twin.binary\tmac.binary"
    s <- sprintf(paste(rep.int("%s", 7L), collapse = "\t"),
                 names(repos),
                 names(repos),
                 repos,
                 rep_len(x$default %||% "TRUE", n),
                 rep_len(x$source  %||% "NA", n),
                 rep_len(x$win.binary %||% "NA", n),
                 rep_len(x$mac.binary %||% "NA", n))
    writeLines(c(h, s), file)
}


### default changed to https: for R 3.3.0
.expand_BioC_repository_URLs <- function(x)
{
    x <- sub("%bm",
             as.character(getOption("BioC_mirror",
                                    "https://bioconductor.org")),
             x, fixed = TRUE)
    sub("%v",
        as.character(.BioC_version_associated_with_R_version()),
        x, fixed = TRUE)
}

## default is included in setRepositories.Rd (via \Sexpr)
.BioC_version_associated_with_R_version_default <- "3.23"
.BioC_version_associated_with_R_version <- function ()
    numeric_version(Sys.getenv("R_BIOC_VERSION",
                               .BioC_version_associated_with_R_version_default))

## Helper for getting the dependencies of the given installed packages
## without reading the DESCRIPTION metadata of all installed packages.
.installed_package_dependencies <- function(pkgs, fields) {
    mat <- do.call(rbind,
                   lapply(.libPaths(), .readPkgDesc, fields, pkgs))
    lst <- apply(mat[, - c(1L, 2L), drop = FALSE], 1L,
                 .clean_up_dependencies, simplify = FALSE)
    names(lst) <- mat[, 1L]
    lst
}
