Add functions for package reverse dependency check #3
Description
As described in http://www.tinyverse.org/, R package dependencies should be as lean as possible. To check wether this is the case for our KWB-R packages the follwing functions should be added to pkgmeta and added to a vignette for automating this analysis (at least for the public R packages).
get_recursive_pkg_dependencies <-
function(pkgs,
library_path = .libPaths(),
dbg = TRUE) {
pkgs_installed <-
pkgs[pkgs %in% rownames(installed.packages(lib.loc = library_path))]
setNames(lapply(pkgs_installed, function(pkg) {
kwb.utils::catAndRun(
sprintf("Getting recursive dependencies for '%s'", pkg),
expr = {
packrat:::recursivePackageDependencies(pkg,
lib.loc = library_path)
},
dbg = dbg
)
}),
nm = pkgs_installed)
}
get_pkg_dependencies <-
function(pkgs,
library_path = .libPaths(),
dbg = TRUE) {
pkgs_installed <-
pkgs[pkgs %in% rownames(installed.packages(lib.loc = library_path))]
setNames(lapply(pkgs_installed, function(pkg) {
kwb.utils::catAndRun(
sprintf("Getting dependencies for '%s'", pkg),
expr = {
packrat:::getPackageDependencies(pkg, lib.loc = library_path)
},
dbg = dbg
)
}),
nm = pkgs_installed)
}
###############################################################################
### Define Function for Installing KWB-R GitHub Packages
###############################################################################
install_kwb_github_packages <- function(pkgs_kwb,
dependencies = TRUE,
...) {
pkgs_kwb_github <- sprintf("KWB-R/%s", pkgs_kwb)
sapply(
pkgs_kwb_github,
FUN = function(gh_repo) {
try(remotes::install_github(repo = gh_repo,
dependencies = dependencies,
...))
}
)
}
###############################################################################
### Use the Install Function For KWB-R Packages
###############################################################################
pkgs <- pkgmeta::get_github_packages()
install_kwb_github_packages(pkgs_kwb = pkgs$name, upgrade = "always")
pkgs_recursive_dependencies <- get_recursive_pkg_dependencies(pkgs$name)
pkgs_dependencies <- get_pkg_dependencies(pkgs$name)
deps_df <- tibble::tibble(package = names(total_deps_per_pkg),
n_dependencies = sapply(pkgs_dependencies, length),
n_recursive_dependencies = sapply(pkgs_recursive_dependencies, length)) %>%
dplyr::arrange(dplyr::desc(n_recursive_dependencies))
Using this locally with GITHUB_PAT with private KWB-R repo scope (installation failed for 2 private repos, see #2), these are the total (recursive) dependencies:
| package | n_dependencies | n_recursive_dependencies |
|---|---|---|
| kwb.flusshygiene.app | 12 | 109 |
| fhpredict | 13 | 107 |
| kwb.flusshygiene | 9 | 100 |
| aquanes.report | 25 | 99 |
| kwb.kuras | 4 | 90 |
| kwb.ogre.model | 5 | 90 |
| kwb.ogre | 10 | 89 |
| kwb.package | 3 | 88 |
| sema.berlin.app | 20 | 88 |
| fakin.path.app | 18 | 86 |
| kwb.dswt | 7 | 86 |
| kwb.endnote | 15 | 84 |
| pkgmeta | 18 | 79 |
| kwb.miacso | 1 | 78 |
| kwb.rain | 5 | 78 |
| kwb.misc | 9 | 77 |
| kwb.qmra | 15 | 76 |
| kwb.read | 7 | 75 |
| datacamp | 21 | 68 |
| kwb.fakin | 20 | 65 |
| kwb.pkgbuild | 13 | 61 |
| sema.berlin | 7 | 55 |
| kwb.twitter | 6 | 52 |
| kwb.umberto | 9 | 52 |
| kwb.monitoring | 8 | 49 |
| kwb.pubs | 10 | 49 |
| AquaNES | 3 | 48 |
| kwb.sema | 7 | 48 |
| kwb.lca | 4 | 46 |
| kwb.dygraph | 3 | 44 |
| kwb.mia.evalCritO2 | 2 | 43 |
| kwb.readxl | 6 | 43 |
| kwb.mia.iw | 6 | 42 |
| kwb.test.datetime | 2 | 42 |
| kwb.base | 6 | 41 |
| kwb.orcid | 5 | 39 |
| kwb.epanet | 4 | 38 |
| kwb.geosalz | 12 | 38 |
| kwb.resilience | 1 | 37 |
| kwb.event | 3 | 36 |
| kwb.pkgstatus | 8 | 36 |
| kwb.site | 4 | 35 |
| kwb.plot | 3 | 34 |
| qmra.db | 10 | 34 |
| kwbGompitz | 3 | 33 |
| kwb.svn | 9 | 31 |
| kwb.test | 2 | 30 |
| kwb.demeau | 9 | 29 |
| kwb.pathdict | 4 | 28 |
| kwb.code | 3 | 27 |
| kwb.file | 5 | 26 |
| kwb.ucode | 1 | 18 |
| kwb.dwd | 10 | 17 |
| kwb.wtaq | 4 | 17 |
| algoliar | 5 | 16 |
| kwb.hantush | 1 | 15 |
| kwb.vs2dh | 4 | 8 |
| kwb.odmx | 3 | 5 |
| kwb.logger | 4 | 4 |
| kwb.odm | 3 | 4 |
| kwb.quantum | 3 | 4 |
| kwb.dwa.m150 | 2 | 3 |
| kwb.context | 2 | 2 |
| kwb.db | 2 | 2 |
| kwb.gocr | 2 | 2 |
| kwb.optiwells | 1 | 2 |
| kwb.rerau | 2 | 2 |
| kwb.datetime | 1 | 1 |
| kwb.en13508.2 | 1 | 1 |
| kwb.graph | 1 | 1 |
| kwb.iview | 1 | 1 |
| kwb.virtualdub | 1 | 1 |
| kwb.barplot | 0 | 0 |
| kwb.default | 0 | 0 |
| kwb.utils | 0 | 0 |