## ------------------------------------------------------------------------
## API
parse_remote_bioc <- function(specs, config, ...) {
## BioC is the same as CRAN, except for cran:: -> bioc::
parsed_specs <- re_match(specs, standard_rx("bioc"))
parsed_specs$ref <- parsed_specs$.text
cn <- setdiff(colnames(parsed_specs), c(".match", ".text"))
parsed_specs <- parsed_specs[, cn]
eq <- parsed_specs$atleast == "" & parsed_specs$version != ""
parsed_specs$atleast[eq] <- "=="
parsed_specs$type <- "bioc"
lapply(
seq_len(nrow(parsed_specs)),
function(i) as.list(parsed_specs[i,])
)
}
resolve_remote_bioc <- function(remote, direct, config, cache,
dependencies, progress_bar, ...) {
force(remote); force(direct); force(dependencies)
versions <- if ("type" %in% names(remote)) {
remote$version
} else {
vcapply(remote, "[[", "version") # nocov
}
if (all(versions %in% c("", "current"))) {
resolve_from_metadata(remote, direct, config, cache, dependencies)
} else {
type_cran_resolve_version(remote, direct, config, cache, dependencies) # nocov
}
}
download_remote_bioc <- function(resolution, target, target_tree, config,
cache, which, on_progress) {
# we need to check if there is a new binary build. for source packages
# we can always use the cache
download_ping_if_not_source(resolution, target, config, cache,
on_progress)
}
satisfy_remote_bioc <- function(resolution, candidate,
config, ...) {
## 1. candidate must be a bioc, standard or installed ref
if (!candidate$type %in% c("bioc", "standard", "installed")) {
return(structure(
FALSE, reason = "Type must be 'bioc', 'standard' or 'installed'"))
}
## 2. installed refs must be from bioc
if (candidate$type == "installed") {
repotype <- candidate$extra[[1]]$repotype
if (! identical(repotype, "bioc")) {
return(structure(FALSE, reason = "Installed package not from BioC"))
}
}
## 3. package names must match
if (resolution$package != candidate$package) {
return(structure(FALSE, reason = "Package names differ"))
}
## 4. installed package must not be older for direct refs
if (resolution$direct) {
if (candidate$type == "installed" &&
package_version(resolution$version) > candidate$version) {
return(structure(FALSE, reason = "Direct ref needs update"))
}
}
## 5. version requirements must be satisfied. Otherwise good.
if (resolution$remote[[1]]$version == "") {
return(TRUE)
}
if (!version_satisfies(
candidate$version,
resolution$remote[[1]]$atleast,
resolution$remote[[1]]$version)) {
return(structure(FALSE, reason = "Insufficient version"))
}
TRUE
}
installedok_remote_bioc <- function(installed, solution, config, ...) {
if (solution$platform != "source") {
# Binary packages are simple. We need to match `$build` to make sure
# that we are installing the same build.
identical(installed$package, solution$package) &&
identical(installed$version, solution$version) &&
installedok_remote_standard_platform(installed, solution, config, ...) &&
identical(installed[["built"]], solution[["built"]])
} else {
# Source packages are different, because only the installed one has a
# 'Built' field.
identical(installed$package, solution$package) &&
identical(installed$version, solution$version) &&
identical(installed[["repotype"]], "bioc")
}
}
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