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install-github.R
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# Autogenerated from contents in the package's R directory, do not edit!
# Run make to update.
function(...) {
## This is the code of the package, put in here by brew
# Contents of R/bioc-standalone.R
#' Tools for Bioconductor versions and repositories
#'
#' \section{API:}
#'
#' ```
#' get_yaml_config(forget = FALSE)
#' set_yaml_config(text)
#'
#' get_release_version(forget = FALSE)
#' get_devel_version(forget = FALSE)
#'
#' get_version_map(forget = FALSE)
#' get_matching_bioc_version(r_version = getRversion(), forget = FALSE)
#' get_bioc_version(r_version = getRversion(), forget = FALSE)
#'
#' get_repos(bioc_version = "auto", forget = FALSE)
#' ```
#'
#' * `forget`: Whether to forget the cached version of the Bioconductor
#' config YAML file and download it again.
#' * `text`: character vector (linewise) or scalar, the contents of the
#' `config.yaml` file, if obtained externally, to be used as a cached
#' version in the future.
#' * `r_version`: R version string, or `package_version` object.
#' * `bioc_version`: Bioc version string or `package_version` object,
#' or the string `"auto"` to use the one matching the current R version.
#'
#' `get_yaml_config()` returns the raw contents of the `config.yaml` file,
#' linewise. It is typically not needed, except if one needs information
#' that cannot be surfaces via the other API functions.
#'
#' `set_yaml_config()` can be used to _set_ the contents of the
#' `config.yaml` file. This is useful, if one has already obtained it
#' externally, but wants to use the obtained file with the rest of the
#' bioc standalone code.
#'
#' `get_release_version()` returns the version of the current Bioconductor
#' release.
#'
#' `get_devel_version()` returns the version of the current development
#' version of Bioconductor.
#'
#' `get_version_map()` return the mapping between R versions and
#' Bioconductor versions. Note that this is not a one to one mapping.
#' E.g. currently R `3.6.x` maps to both Bioc `3.9` (Bioc release) and
#' `3.10` (Bioc devel); and also Bioc `3.10` maps to both R `3.6.x` and
#' R `3.7.x` (current R-devel). It returns a data frame with three columns:
#' `bioc_version`, `r_version` and `bioc_status`. The first two columns
#' contain `package_vesion` objects, the third is a factor with levels:
#' `out-of-date`, `release`, `devel`, `future`.
#'
#' `get_matching_bioc_version()` returns the matching Bioc version for an
#' R version. If the R version matches to both a released and a devel
#' version, then the released version is chosen.
#'
#' `get_bioc_version()` returns the matching Bioc version for the
#' specified R version. It does observe the `R_BIOC_VERSION` environment
#' variable, which can be used to force a Bioconductor version. If this is
#' not set, it just calls `get_matching_bioc_version()`.
#'
#' `get_repos()` returns the Bioc repositories of the specified Bioc
#' version. It defaults to the Bioc version that matches the calling R
#' version. It returns a named character vector.
#'
#' \section{NEWS:}
#' * 2019-05-30 First version in remotes.
#' * 2020-03-22 get_matching_bioc_version() is now correct if the current
#' R version is not in the builtin mapping.
#'
#' @name bioconductor
#' @keywords internal
#' @noRd
NULL
bioconductor <- local({
# -------------------------------------------------------------------
# Configuration that does not change often
config_url <- "https://bioconductor.org/config.yaml"
builtin_map <- list(
"2.1" = package_version("1.6"),
"2.2" = package_version("1.7"),
"2.3" = package_version("1.8"),
"2.4" = package_version("1.9"),
"2.5" = package_version("2.0"),
"2.6" = package_version("2.1"),
"2.7" = package_version("2.2"),
"2.8" = package_version("2.3"),
"2.9" = package_version("2.4"),
"2.10" = package_version("2.5"),
"2.11" = package_version("2.6"),
"2.12" = package_version("2.7"),
"2.13" = package_version("2.8"),
"2.14" = package_version("2.9"),
"2.15" = package_version("2.11"),
"3.0" = package_version("2.13"),
"3.1" = package_version("3.0"),
"3.2" = package_version("3.2"),
"3.3" = package_version("3.4"),
"3.4" = package_version("3.6"),
"3.5" = package_version("3.8"),
"3.6" = package_version("3.10")
)
# -------------------------------------------------------------------
# Cache
devel_version <- NULL
release_version <- NULL
version_map <- NULL
yaml_config <- NULL
# -------------------------------------------------------------------
# API
get_yaml_config <- function(forget = FALSE) {
if (forget || is.null(yaml_config)) {
new <- tryCatch(read_url(config_url), error = function(x) x)
if (inherits(new, "error")) {
http_url <- sub("^https", "http", config_url)
new <- tryCatch(read_url(http_url), error = function(x) x)
}
if (inherits(new, "error")) stop(new)
yaml_config <<- new
}
yaml_config
}
set_yaml_config <- function(text) {
if (length(text) == 1) text <- strsplit(text, "\n", fixed = TRUE)[[1]]
yaml_config <<- text
}
get_release_version <- function(forget = FALSE) {
if (forget || is.null(release_version)) {
yaml <- get_yaml_config(forget)
pattern <- "^release_version: \"(.*)\""
release_version <<- package_version(
sub(pattern, "\\1", grep(pattern, yaml, value=TRUE))
)
}
release_version
}
get_devel_version <- function(forget = FALSE) {
if (forget || is.null(devel_version)) {
yaml <- get_yaml_config(forget)
pattern <- "^devel_version: \"(.*)\""
devel_version <<- package_version(
sub(pattern, "\\1", grep(pattern, yaml, value=TRUE))
)
}
devel_version
}
get_version_map <- function(forget = FALSE) {
if (forget || is.null(version_map)) {
txt <- get_yaml_config(forget)
grps <- grep("^[^[:blank:]]", txt)
start <- match(grep("r_ver_for_bioc_ver", txt), grps)
map <- txt[seq(grps[start] + 1, grps[start + 1] - 1)]
map <- trimws(gsub("\"", "", sub(" #.*", "", map)))
pattern <- "(.*): (.*)"
bioc <- package_version(sub(pattern, "\\1", map))
r <- package_version(sub(pattern, "\\2", map))
status <- rep("out-of-date", length(bioc))
release <- get_release_version()
devel <- get_devel_version()
status[bioc == release] <- "release"
status[bioc == devel] <- "devel"
# append final version for 'devel' R
bioc <- c(
bioc, max(bioc)
)
r <- c(r, package_version(paste(unlist(max(r)) + 0:1, collapse = ".")))
status <- c(status, "future")
version_map <<- rbind(
.VERSION_MAP_SENTINEL,
data.frame(
bioc_version = bioc, r_version = r,
bioc_status = factor(
status,
levels = c("out-of-date", "release", "devel", "future")
)
)
)
}
version_map
}
get_matching_bioc_version <- function(r_version = getRversion(),
forget = FALSE) {
minor <- as.character(get_minor_r_version(r_version))
if (minor %in% names(builtin_map)) return(builtin_map[[minor]])
# If we are not in the map, then we need to look this up in
# YAML data. It is possible that the current R version matches multiple
# Bioc versions. Then we choose the latest released version. If none
# of them were released (e.g. they are 'devel' and 'future'), then
# we'll use the 'devel' version.
map <- get_version_map(forget = forget)
mine <- which(package_version(minor) == map$r_version)
if (length(mine) == 0) {
mine <- NA
} else if (length(mine) > 1) {
if ("release" %in% map$bioc_status[mine]) {
mine <- mine["release" == map$bioc_status[mine]]
} else if ("devel" %in% map$bioc_status[mine]) {
mine <- mine["devel" == map$bioc_status[mine]]
} else {
mine <- rev(mine)[1]
}
}
if (!is.na(mine)) return(map$bioc_version[mine])
# If it is not even in the YAML, then it must be some very old
# or very new version. If old, we fail. If new, we assume bioc-devel.
if (package_version(minor) < "2.1") {
stop("R version too old, cannot run Bioconductor")
}
get_devel_version()
}
get_bioc_version <- function(r_version = getRversion(),
forget = FALSE) {
if (nzchar(v <- Sys.getenv("R_BIOC_VERSION", ""))) {
return(package_version(v))
}
get_matching_bioc_version(r_version, forget = forget)
}
get_repos <- function(bioc_version = "auto", forget = FALSE) {
if (identical(bioc_version, "auto")) {
bioc_version <- get_bioc_version(getRversion(), forget)
} else {
bioc_version <- package_version(bioc_version)
}
mirror <- Sys.getenv("R_BIOC_MIRROR", "https://bioconductor.org")
mirror <- getOption("BioC_mirror", mirror)
repos <- c(
BioCsoft = "{mirror}/packages/{bv}/bioc",
BioCann = "{mirror}/packages/{bv}/data/annotation",
BioCexp = "{mirror}/packages/{bv}/data/experiment",
BioCworkflows =
if (bioc_version >= "3.7") "{mirror}/packages/{bv}/workflows",
BioCextra =
if (bioc_version <= "3.5") "{mirror}/packages/{bv}/extra"
)
## It seems that if a repo is not available yet for bioc-devel,
## they redirect to the bioc-release version, so we do not need to
## parse devel_repos from the config.yaml file
sub("{mirror}", mirror, fixed = TRUE,
sub("{bv}", bioc_version, repos, fixed = TRUE))
}
# -------------------------------------------------------------------
# Internals
read_url <- function(url) {
tmp <- tempfile()
on.exit(unlink(tmp), add = TRUE)
suppressWarnings(download.file(url, tmp, quiet = TRUE))
if (!file.exists(tmp) || file.info(tmp)$size == 0) {
stop("Failed to download `", url, "`")
}
readLines(tmp, warn = FALSE)
}
.VERSION_SENTINEL <- local({
version <- package_version(list())
class(version) <- c("unknown_version", class(version))
version
})
.VERSION_MAP_SENTINEL <- data.frame(
bioc_version = .VERSION_SENTINEL,
r_version = .VERSION_SENTINEL,
bioc_status = factor(
factor(),
levels = c("out-of-date", "release", "devel", "future")
)
)
get_minor_r_version <- function (x) {
package_version(x)[,1:2]
}
# -------------------------------------------------------------------
structure(
list(
.internal = environment(),
get_yaml_config = get_yaml_config,
set_yaml_config = set_yaml_config,
get_release_version = get_release_version,
get_devel_version = get_devel_version,
get_version_map = get_version_map,
get_matching_bioc_version = get_matching_bioc_version,
get_bioc_version = get_bioc_version,
get_repos = get_repos
),
class = c("standalone_bioc", "standalone"))
})
# Contents of R/bioc.R
#' @export
#' @rdname bioc_install_repos
#' @keywords internal
#' @examples
#' bioc_version()
#' bioc_version("3.4")
bioc_version <- function(r_ver = getRversion()) {
bioconductor$get_bioc_version(r_ver)
}
#' Tools for Bioconductor repositories
#'
#' `bioc_version()` returns the Bioconductor version for the current or the
#' specified R version.
#'
#' `bioc_install_repos()` deduces the URLs of the Bioconductor repositories.
#'
#' @details
#' Both functions observe the `R_BIOC_VERSION` environment variable, which
#' can be set to force a Bioconductor version. If this is set, then the
#' `r_ver` and `bioc_ver` arguments are ignored.
#'
#' `bioc_install_repos()` observes the `R_BIOC_MIRROR` environment variable
#' and also the `BioC_mirror` option, which can be set to the desired
#' Bioconductor mirror. The option takes precedence if both are set. Its
#' default value is `https://bioconductor.org`.
#'
#' @return
#' `bioc_version()` returns a Bioconductor version, a `package_version`
#' object.
#'
#' `bioc_install_repos()` returns a named character vector of the URLs of
#' the Bioconductor repositories, appropriate for the current or the
#' specified R version.
#'
#' @param r_ver R version to use. For `bioc_install_repos()` it is
#' ignored if `bioc_ver` is specified.
#' @param bioc_ver Bioconductor version to use. Defaults to the default one
#' corresponding to `r_ver`.
#'
#' @export
#' @keywords internal
#' @examples
#' bioc_install_repos()
bioc_install_repos <- function(r_ver = getRversion(),
bioc_ver = bioc_version(r_ver)) {
bioconductor$get_repos(bioc_ver)
}
# Contents of R/circular.R
## A environment to hold which packages are being installed so packages
## with circular dependencies can be skipped the second time.
installing <- new.env(parent = emptyenv())
is_root_install <- function() is.null(installing$packages)
exit_from_root_install <- function() installing$packages <- NULL
check_for_circular_dependencies <- function(pkgdir, quiet) {
pkgdir <- normalizePath(pkgdir)
pkg <- get_desc_field(file.path(pkgdir, "DESCRIPTION"), "Package")
if (pkg %in% installing$packages) {
if (!quiet) message("Skipping ", pkg, ", it is already being installed")
TRUE
} else {
installing$packages <- c(installing$packages, pkg)
FALSE
}
}
# Contents of R/cran.R
cache <- new.env(parent = emptyenv())
#' @rdname available_packages
#' @export
available_packages_set <- function(repos, type, db) {
signature <- rawToChar(serialize(list(repos, type), NULL, ascii = TRUE))
if (is.null(cache[[signature]])) {
cache[[signature]] <- db
}
cache[[signature]]
}
#' @rdname available_packages
#' @export
available_packages_reset <- function() {
rm(list = ls(envir = cache), envir = cache)
}
#' Simpler available.packages
#'
#' This is mostly equivalent to [utils::available.packages()] however it also
#' caches the full result. Additionally the cache can be assigned explicitly with
#' [available_packages_set()] and reset (cleared) with [available_packages_reset()].
#'
#' @inheritParams utils::available.packages
#' @keywords internal
#' @seealso [utils::available.packages()] for full documentation on the output format.
#' @export
available_packages <- function(repos = getOption("repos"), type = getOption("pkgType")) {
available_packages_set(
repos, type,
suppressWarnings(utils::available.packages(utils::contrib.url(repos, type), type = type))
)
}
# Contents of R/dcf.R
read_dcf <- function(path) {
fields <- colnames(read.dcf(path))
as.list(read.dcf(path, keep.white = fields)[1, ])
}
write_dcf <- function(path, desc) {
write.dcf(
rbind(unlist(desc)),
file = path,
keep.white = names(desc),
indent = 0
)
}
get_desc_field <- function(path, field) {
dcf <- read_dcf(path)
dcf[[field]]
}
# Contents of R/decompress.R
# Decompress pkg, if needed
source_pkg <- function(path, subdir = NULL) {
if (!dir.exists(path)) {
bundle <- path
outdir <- tempfile(pattern = "remotes")
dir.create(outdir)
path <- decompress(path, outdir)
} else {
bundle <- NULL
}
pkg_path <- if (is.null(subdir)) path else file.path(path, subdir)
# Check it's an R package
if (!file.exists(file.path(pkg_path, "DESCRIPTION"))) {
stop("Does not appear to be an R package (no DESCRIPTION)", call. = FALSE)
}
# Check configure is executable if present
config_path <- file.path(pkg_path, "configure")
if (file.exists(config_path)) {
Sys.chmod(config_path, "777")
}
pkg_path
}
decompress <- function(src, target) {
stopifnot(file.exists(src))
if (grepl("\\.zip$", src)) {
my_unzip(src, target)
outdir <- getrootdir(as.vector(utils::unzip(src, list = TRUE)$Name))
} else if (grepl("\\.(tar|tar\\.gz|tar\\.bz2|tgz|tbz)$", src)) {
untar(src, exdir = target)
outdir <- getrootdir(untar(src, list = TRUE))
} else {
ext <- gsub("^[^.]*\\.", "", src)
stop("Don't know how to decompress files with extension ", ext,
call. = FALSE)
}
file.path(target, outdir)
}
# Returns everything before the last slash in a filename
# getdir("path/to/file") returns "path/to"
# getdir("path/to/dir/") returns "path/to/dir"
getdir <- function(path) sub("/[^/]*$", "", path)
# Given a list of files, returns the root (the topmost folder)
# getrootdir(c("path/to/file", "path/to/other/thing")) returns "path/to"
# It does not check that all paths have a common prefix. It fails for
# empty input vector. It assumes that directories end with '/'.
getrootdir <- function(file_list) {
stopifnot(length(file_list) > 0)
slashes <- nchar(gsub("[^/]", "", file_list))
if (min(slashes) == 0) return(".")
getdir(file_list[which.min(slashes)])
}
my_unzip <- function(src, target, unzip = getOption("unzip", "internal")) {
if (unzip %in% c("internal", "")) {
return(utils::unzip(src, exdir = target))
}
args <- paste(
"-oq", shQuote(src),
"-d", shQuote(target)
)
system_check(unzip, args)
}
# Contents of R/deps.R
#' Find all dependencies of a CRAN or dev package.
#'
#' Find all the dependencies of a package and determine whether they are ahead
#' or behind CRAN. A `print()` method identifies mismatches (if any)
#' between local and CRAN versions of each dependent package; an
#' `update()` method installs outdated or missing packages from CRAN.
#'
#' @param packages A character vector of package names.
#' @param pkgdir path to a package directory, or to a package tarball.
#' @param dependencies Which dependencies do you want to check?
#' Can be a character vector (selecting from "Depends", "Imports",
#' "LinkingTo", "Suggests", or "Enhances"), or a logical vector.
#'
#' `TRUE` is shorthand for "Depends", "Imports", "LinkingTo" and
#' "Suggests". `NA` is shorthand for "Depends", "Imports" and "LinkingTo"
#' and is the default. `FALSE` is shorthand for no dependencies (i.e.
#' just check this package, not its dependencies).
#' @param quiet If `TRUE`, suppress output.
#' @param upgrade One of "default", "ask", "always", or "never". "default"
#' respects the value of the `R_REMOTES_UPGRADE` environment variable if set,
#' and falls back to "ask" if unset. "ask" prompts the user for which out of
#' date packages to upgrade. For non-interactive sessions "ask" is equivalent
#' to "always". `TRUE` and `FALSE` are also accepted and correspond to
#' "always" and "never" respectively.
#' @param repos A character vector giving repositories to use.
#' @param type Type of package to `update`.
#'
#' @param object A `package_deps` object.
#' @param ... Additional arguments passed to `install_packages`.
#' @inheritParams install_github
#'
#' @return
#'
#' A `data.frame` with columns:
#'
#' \tabular{ll}{
#' `package` \tab The dependent package's name,\cr
#' `installed` \tab The currently installed version,\cr
#' `available` \tab The version available on CRAN,\cr
#' `diff` \tab An integer denoting whether the locally installed version
#' of the package is newer (1), the same (0) or older (-1) than the version
#' currently available on CRAN.\cr
#' }
#'
#' @export
#' @examples
#' \dontrun{
#' package_deps("devtools")
#' # Use update to update any out-of-date dependencies
#' update(package_deps("devtools"))
#' }
package_deps <- function(packages, dependencies = NA,
repos = getOption("repos"),
type = getOption("pkgType")) {
repos <- fix_repositories(repos)
cran <- available_packages(repos, type)
deps <- find_deps(packages, available = cran, top_dep = dependencies)
# Remove base packages
inst <- utils::installed.packages()
base <- unname(inst[inst[, "Priority"] %in% c("base", "recommended"), "Package"])
deps <- setdiff(deps, base)
# get remote types
remote <- structure(lapply(deps, package2remote, repos = repos, type = type), class = "remotes")
inst_ver <- vapply(deps, local_sha, character(1))
cran_ver <- vapply(remote, function(x) remote_sha(x), character(1))
is_cran_remote <- vapply(remote, inherits, logical(1), "cran_remote")
diff <- compare_versions(inst_ver, cran_ver, is_cran_remote)
res <- structure(
data.frame(
package = deps,
installed = inst_ver,
available = cran_ver,
diff = diff,
is_cran = is_cran_remote,
stringsAsFactors = FALSE
),
class = c("package_deps", "data.frame")
)
res$remote <- remote
res
}
#' `local_package_deps` extracts dependencies from a
#' local DESCRIPTION file.
#'
#' @export
#' @rdname package_deps
local_package_deps <- function(pkgdir = ".", dependencies = NA) {
pkg <- load_pkg_description(pkgdir)
dependencies <- tolower(standardise_dep(dependencies))
dependencies <- intersect(dependencies, names(pkg))
parsed <- lapply(pkg[tolower(dependencies)], parse_deps)
unlist(lapply(parsed, `[[`, "name"), use.names = FALSE)
}
#' `dev_package_deps` lists the status of the dependencies
#' of a local package.
#'
#' @export
#' @rdname package_deps
dev_package_deps <- function(pkgdir = ".", dependencies = NA,
repos = getOption("repos"),
type = getOption("pkgType")) {
pkg <- load_pkg_description(pkgdir)
repos <- c(repos, parse_additional_repositories(pkg))
deps <- local_package_deps(pkgdir = pkgdir, dependencies = dependencies)
if (is_bioconductor(pkg)) {
bioc_repos <- bioc_install_repos()
missing_repos <- setdiff(names(bioc_repos), names(repos))
if (length(missing_repos) > 0)
repos[missing_repos] <- bioc_repos[missing_repos]
}
combine_deps(
package_deps(deps, repos = repos, type = type),
remote_deps(pkg))
}
combine_deps <- function(cran_deps, remote_deps) {
# If there are no dependencies there will be no remote dependencies either,
# so just return them (and don't force the remote_deps promise)
if (nrow(cran_deps) == 0) {
return(cran_deps)
}
# Only keep the remotes that are specified in the cran_deps or are NA
remote_deps <- remote_deps[is.na(remote_deps$package) | remote_deps$package %in% cran_deps$package, ]
# If there are remote deps remove the equivalent CRAN deps
cran_deps <- cran_deps[!(cran_deps$package %in% remote_deps$package), ]
rbind(remote_deps, cran_deps)
}
## -2 = not installed, but available on CRAN
## -1 = installed, but out of date
## 0 = installed, most recent version
## 1 = installed, version ahead of CRAN
## 2 = package not on CRAN
compare_versions <- function(inst, remote, is_cran) {
stopifnot(length(inst) == length(remote) && length(inst) == length(is_cran))
compare_var <- function(i, c, cran) {
if (!cran) {
if (identical(i, c)) {
return(CURRENT)
} else {
return(BEHIND)
}
}
if (is.na(c)) return(UNAVAILABLE) # not on CRAN
if (is.na(i)) return(UNINSTALLED) # not installed, but on CRAN
i <- package_version(i)
c <- package_version(c)
if (i < c) {
BEHIND # out of date
} else if (i > c) {
AHEAD # ahead of CRAN
} else {
CURRENT # most recent CRAN version
}
}
vapply(seq_along(inst),
function(i) compare_var(inst[[i]], remote[[i]], is_cran[[i]]),
integer(1))
}
has_dev_remotes <- function(pkg) {
!is.null(pkg[["remotes"]])
}
#' @export
print.package_deps <- function(x, show_ok = FALSE, ...) {
class(x) <- "data.frame"
x$remote <-lapply(x$remote, format)
ahead <- x$diff > 0L
behind <- x$diff < 0L
same_ver <- x$diff == 0L
x$diff <- NULL
x[] <- lapply(x, format_str, width = 12)
if (any(behind)) {
cat("Needs update -----------------------------\n")
print(x[behind, , drop = FALSE], row.names = FALSE, right = FALSE)
}
if (any(ahead)) {
cat("Not on CRAN ----------------------------\n")
print(x[ahead, , drop = FALSE], row.names = FALSE, right = FALSE)
}
if (show_ok && any(same_ver)) {
cat("OK ---------------------------------------\n")
print(x[same_ver, , drop = FALSE], row.names = FALSE, right = FALSE)
}
}
## -2 = not installed, but available on CRAN
## -1 = installed, but out of date
## 0 = installed, most recent version
## 1 = installed, version ahead of CRAN
## 2 = package not on CRAN
UNINSTALLED <- -2L
BEHIND <- -1L
CURRENT <- 0L
AHEAD <- 1L
UNAVAILABLE <- 2L
#' @export
#' @rdname package_deps
#' @importFrom stats update
update.package_deps <- function(object,
dependencies = NA,
upgrade = c("default", "ask", "always", "never"),
force = FALSE,
quiet = FALSE,
build = TRUE, build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"),
build_manual = FALSE, build_vignettes = FALSE,
repos = getOption("repos"),
type = getOption("pkgType"),
...) {
object <- upgradable_packages(object, upgrade, quiet)
unavailable_on_cran <- object$diff == UNAVAILABLE & object$is_cran
unknown_remotes <- (object$diff == UNAVAILABLE | object$diff == UNINSTALLED) & !object$is_cran
if (any(unavailable_on_cran) && !quiet) {
message("Skipping ", sum(unavailable_on_cran), " packages not available: ",
paste(object$package[unavailable_on_cran], collapse = ", "))
}
if (any(unknown_remotes)) {
install_remotes(object$remote[unknown_remotes],
dependencies = dependencies,
upgrade = upgrade,
force = force,
quiet = quiet,
build = build,
build_opts = build_opts,
build_manual = build_manual,
build_vignettes = build_vignettes,
repos = repos,
type = type,
...)
}
ahead_of_cran <- object$diff == AHEAD & object$is_cran
if (any(ahead_of_cran) && !quiet) {
message("Skipping ", sum(ahead_of_cran), " packages ahead of CRAN: ",
paste(object$package[ahead_of_cran], collapse = ", "))
}
ahead_remotes <- object$diff == AHEAD & !object$is_cran
if (any(ahead_remotes)) {
install_remotes(object$remote[ahead_remotes],
dependencies = dependencies,
upgrade = upgrade,
force = force,
quiet = quiet,
build = build,
build_opts = build_opts,
build_manual = build_manual,
build_vignettes = build_vignettes,
repos = repos,
type = type,
...)
}
behind <- is.na(object$installed) | object$diff < CURRENT
if (any(object$is_cran & !unavailable_on_cran & behind)) {
# get the first cran-like remote and use its repos and pkg_type
r <- object$remote[object$is_cran & behind][[1]]
install_packages(object$package[object$is_cran & behind], repos = r$repos,
type = r$pkg_type, dependencies = dependencies, quiet = quiet, ...)
}
install_remotes(object$remote[!object$is_cran & behind],
dependencies = dependencies,
upgrade = upgrade,
force = force,
quiet = quiet,
build = build,
build_opts = build_opts,
build_manual = build_manual,
build_vignettes = build_vignettes,
repos = repos,
type = type,
...)
invisible()
}
install_packages <- function(packages, repos = getOption("repos"),
type = getOption("pkgType"), ...,
dependencies = FALSE, quiet = NULL) {
# We want to pass only args that exist in the downstream functions
args_to_keep <-
unique(
names(
c(
formals(utils::install.packages),
formals(utils::download.file)
)
)
)
args <- list(...)
args <- args[names(args) %in% args_to_keep]
if (is.null(quiet))
quiet <- !identical(type, "source")
message("Installing ", length(packages), " packages: ",
paste(packages, collapse = ", "))
do.call(
safe_install_packages,
c(list(
packages,
repos = repos,
type = type,
dependencies = dependencies,
quiet = quiet
),
args
)
)
}
find_deps <- function(packages, available = available_packages(),
top_dep = TRUE, rec_dep = NA, include_pkgs = TRUE) {
if (length(packages) == 0 || identical(top_dep, FALSE))
return(character())
top_dep <- standardise_dep(top_dep)
rec_dep <- standardise_dep(rec_dep)
top <- tools::package_dependencies(packages, db = available, which = top_dep)
top_flat <- unlist(top, use.names = FALSE)
if (length(rec_dep) != 0 && length(top_flat) > 0) {
rec <- tools::package_dependencies(top_flat, db = available, which = rec_dep,
recursive = TRUE)
rec_flat <- unlist(rec, use.names = FALSE)
} else {
rec_flat <- character()
}
# We need to put the recursive dependencies _before_ the top dependencies and
# input packages, to ensure that any dependencies are installed before
# their parents are loaded.
unique(c(rec_flat, top_flat, if (include_pkgs) packages))
}
#' Standardise dependencies using the same logical as [install.packages]
#'
#' @param x The dependencies to standardise.
#' A character vector (selecting from "Depends", "Imports",
#' "LinkingTo", "Suggests", or "Enhances"), or a logical vector.
#'
#' `TRUE` is shorthand for "Depends", "Imports", "LinkingTo" and
#' "Suggests". `NA` is shorthand for "Depends", "Imports" and "LinkingTo"
#' and is the default. `FALSE` is shorthand for no dependencies.
#'
#' @seealso <http://r-pkgs.had.co.nz/description.html#dependencies> for
#' additional information on what each dependency type means.
#' @keywords internal
#' @export
standardise_dep <- function(x) {
if (identical(x, NA)) {
c("Depends", "Imports", "LinkingTo")
} else if (isTRUE(x)) {
c("Depends", "Imports", "LinkingTo", "Suggests")
} else if (identical(x, FALSE)) {
character(0)
} else if (is.character(x)) {
x
} else {
stop("Dependencies must be a boolean or a character vector", call. = FALSE)
}
}
#' Update packages that are missing or out-of-date.
#'
#' Works similarly to [utils::install.packages()] but doesn't install packages
#' that are already installed, and also upgrades out dated dependencies.
#'
#' @param packages Character vector of packages to update.
#' @inheritParams install_github
#' @seealso [package_deps()] to see which packages are out of date/
#' missing.
#' @export
#' @examples
#' \dontrun{
#' update_packages("ggplot2")
#' update_packages(c("plyr", "ggplot2"))
#' }
update_packages <- function(packages = TRUE,
dependencies = NA,
upgrade = c("default", "ask", "always", "never"),
force = FALSE,
quiet = FALSE,
build = TRUE, build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"),
build_manual = FALSE, build_vignettes = FALSE,
repos = getOption("repos"),
type = getOption("pkgType"),
...) {
if (isTRUE(packages)) {
packages <- utils::installed.packages()[, "Package"]
}
pkgs <- package_deps(packages, repos = repos, type = type)
update(pkgs,
dependencies = dependencies,
upgrade = upgrade,
force = force,
quiet = quiet,
build = build,
build_opts = build_opts,
build_manual = build_manual,
build_vignettes = build_vignettes,
repos = repos,
type = type,
...)
}
has_additional_repositories <- function(pkg) {
"additional_repositories" %in% names(pkg)
}
parse_additional_repositories <- function(pkg) {
if (has_additional_repositories(pkg)) {
strsplit(trim_ws(pkg[["additional_repositories"]]), "[,[:space:]]+")[[1]]