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Install Suggested package after package installation #1184

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May 26, 2016
Merged

Install Suggested package after package installation #1184

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5f8428c
Install Suggested package after package installation
jimhester May 10, 2016
7f54aaf
cache result of remote_deps() so we don't query it twice
jimhester May 11, 2016
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13 changes: 10 additions & 3 deletions R/deps.R
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Original file line number Diff line number Diff line change
Expand Up @@ -111,14 +111,21 @@ dev_package_deps <- function(pkg = ".", dependencies = NA,
repos[missing_repos] <- bioc_repos[missing_repos]
}

filter_duplicate_deps(
res <- filter_duplicate_deps(
package_deps(deps, repos = repos, type = type),
remote_deps(pkg))

# We set this cache in install() so we can run install_deps() twice without
# having to re-query the remotes
installing$remote_deps %||% remote_deps(pkg))

# Only keep dependencies we actually want to use
res[res$package %in% deps, ]
}

filter_duplicate_deps <- function(cran_deps, remote_deps) {
filter_duplicate_deps <- function(cran_deps, remote_deps, dependencies) {
deps <- rbind(cran_deps, remote_deps)

# Only keep the remotes that are specified in the cran_deps
# Keep only the Non-CRAN remotes if there are duplicates as we want to install
# the development version rather than the CRAN version. The remotes will
# always be specified after the CRAN dependencies, so using fromLast will
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20 changes: 17 additions & 3 deletions R/install.r
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Expand Up @@ -96,9 +96,20 @@ install <-

# If building vignettes, make sure we have all suggested packages too.
if (build_vignettes && missing(dependencies)) {
dependencies <- TRUE
dependencies <- standardise_dep(TRUE)
} else {
dependencies <- standardise_dep(dependencies)
}
install_deps(pkg, dependencies = dependencies, upgrade = upgrade_dependencies,

initial_deps <- dependencies[dependencies != "Suggests"]
final_deps <- dependencies[dependencies == "Suggests"]
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What about "Enhances"?

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I think Enhances should be fine to installed in the initial installation. Note Enhances: are not installed unless explicitly set by default (see ?install.packages).

logical indicating whether to also install uninstalled
packages which these packages depend on/link
to/import/suggest (and so on recursively). Not used if
‘repos = NULL’. Can also be a character vector, a subset of
‘c("Depends", "Imports", "LinkingTo", "Suggests",
"Enhances")’

Only supported if ‘lib’ is of length one (or missing), so it is
unambiguous where to install the dependent packages. If this is not the case
it is ignored, with a warning.

The default, ‘NA’, means ‘c("Depends", "Imports",
"LinkingTo")’.

‘TRUE’ means to use ‘c("Depends", "Imports", "LinkingTo",
"Suggests")’ for ‘pkgs’ and ‘c("Depends", "Imports",
"LinkingTo")’ for added dependencies: this installs all the
packages needed to run ‘pkgs’, their examples, tests and
vignettes (if the package author specified them correctly).

In all of these, ‘"LinkingTo"’ is omitted for binary
packages.

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What happens if there's a dependency chain like A -> (enhances) B -> (imports) A and I try to install(A) or install_deps(A)?


# cache the Remote: dependencies here so we don't have to query them each
# time we call install_deps
installing$remote_deps <- remote_deps(pkg)
on.exit(installing$remote_deps <- NULL, add = TRUE)

install_deps(pkg, dependencies = initial_deps, upgrade = upgrade_dependencies,
threads = threads, force_deps = force_deps, quiet = quiet, ...)

# Build the package. Only build locally if it doesn't have vignettes
Expand All @@ -107,7 +118,7 @@ install <-
built_path <- pkg$path
} else {
built_path <- build(pkg, tempdir(), vignettes = build_vignettes, quiet = quiet)
on.exit(unlink(built_path))
on.exit(unlink(built_path), add = TRUE)
}

opts <- c(
Expand All @@ -124,6 +135,9 @@ install <-
R(paste("CMD INSTALL ", shQuote(built_path), " ", opts, sep = ""),
quiet = quiet)

install_deps(pkg, dependencies = final_deps, upgrade = upgrade_dependencies,
threads = threads, force_deps = force_deps, quiet = quiet, ...)

if (length(metadata) > 0) {
add_metadata(inst(pkg$package), metadata)
}
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