Package 'staged.dependencies' reference manual

Title:	Install R packages from Particular Git Branches
Description:	When developing multiple dependent packages, it is often useful to introduce development stages (devel, pre-release, release) that synchronize these packages. This package provides an implementation of development stages via branch naming rules. It defines RStudio addins that allow to install the matching upstream and downstream dependencies.
Authors:	Adrian Waddell [aut, cre], Maximilian Mordig [aut], Nikolas Burkoff [aut]
Maintainer:	Adrian Waddell <[email protected]>
License:	file LICENSE
Version:	0.3.1.9001
Built:	2024-12-06 03:11:07 UTC
Source:	https://github.com/openpharma/staged.dependencies

Build, check and install internal dependencies

Description

Build, check and install internal dependencies

Usage

build_check_install(
  dep_structure,
  install_direction = "all",
  steps = c("build", "check", "install"),
  rcmd_args = list(check = c("--no-multiarch", "--with-keep.source", "--install-tests")),
  artifact_dir = tempfile(),
  install_external_deps = TRUE,
  upgrade = "never",
  package_list = NULL,
  dry = FALSE,
  verbose = 1,
  ...
)
build_check_install(
  dep_structure,
  install_direction = "all",
  steps = c("build", "check", "install"),
  rcmd_args = list(check = c("--no-multiarch", "--with-keep.source", "--install-tests")),
  artifact_dir = tempfile(),
  install_external_deps = TRUE,
  upgrade = "never",
  package_list = NULL,
  dry = FALSE,
  verbose = 1,
  ...
)

Arguments

`dep_structure`	(`dependency_structure`) output of function `dependency_table`; uses `dep_structure$table` to infer the packages to apply action to and infer installation order; uses `dep_structure$deps` to infer upstream dependencies
`install_direction`	"upstream", "downstream" or "all"; which packages to install (according to dependency structure). By default this is only "upstream"
`steps`	(`character` vector) subset of "build", "check", "install"; useful to skip checking for example
`rcmd_args`	(`list`) with names `build`, `check`, `install` which are vectors that are passed as separate arguments to the `⁠R CMD⁠` commands
`artifact_dir`	(`character`) directory to place built R packages and logs
`install_external_deps`	logical to describe whether to install external dependencies of package using `remotes::install_deps()` (or `renv::install()` if inside an renv environment) .
`upgrade`	argument passed to `remotes::install_deps()`, defaults to `'never'`. Ignored if inside an `renv` environment.
`package_list`	(`character`) If not NULL, an additional filter, only packages on this list will be considered and their dependencies installed if needed (advanced usage only).
`dry`	(`logical`) dry run that outputs what would happen without actually doing it.
`verbose`	(`numeric`) verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)
`...`	Arguments passed on to `install_deps` `install_project` (`logical`) whether to also install the current package (i.e. the package named in `dependency_structure$current_pkg`), ignored unless `install_direction = "upstream"` (because downstream deps automatically install all their upstream deps)

Value

list with entries

artifact_dir: artifact_dir directory with log files
pkg_actions: data.frame of performed actions

Examples

## Not run: 
x <- dependency_table(project = ".", verbose = 1)
build_check_install(x, steps = c("build", "check"), verbose = 1)
build_check_install(x, artifact_dir = "../output")

## End(Not run)
## Not run: 
x <- dependency_table(project = ".", verbose = 1)
build_check_install(x, steps = c("build", "check"), verbose = 1)
build_check_install(x, artifact_dir = "../output")

## End(Not run)

Check & install downstream dependencies

Description

Installs downstream R packages as specified in a dependency_structure object and then runs rcmdcheck (⁠R CMD check⁠) on the downstream dependencies.

Usage

check_downstream(
  dep_structure,
  distance = NULL,
  check_args = c("--no-multiarch", "--with-keep.source", "--install-tests"),
  only_tests = FALSE,
  install_external_deps = TRUE,
  upgrade = "never",
  package_list = NULL,
  dry = FALSE,
  verbose = 1,
  ...
)
check_downstream(
  dep_structure,
  distance = NULL,
  check_args = c("--no-multiarch", "--with-keep.source", "--install-tests"),
  only_tests = FALSE,
  install_external_deps = TRUE,
  upgrade = "never",
  package_list = NULL,
  dry = FALSE,
  verbose = 1,
  ...
)

Arguments

`dep_structure`	(`dependency_structure`) output of function `dependency_table`; uses `dep_structure$table` to infer the packages to apply action to and infer installation order; uses `dep_structure$deps` to infer upstream dependencies
`distance`	(`numeric`) additional filter to only install downstream packages at most this distance from the `dependency_structure$current_pkg` (advanced use only)
`check_args`	(`list`) arguments passed to `rcmdcheck`
`only_tests`	(`logical`) whether to only run tests (rather than checks)
`install_external_deps`	logical to describe whether to install external dependencies of package using `remotes::install_deps()` (or `renv::install()` if inside an renv environment) .
`upgrade`	argument passed to `remotes::install_deps()`, defaults to `'never'`. Ignored if inside an `renv` environment.
`package_list`	(`character`) If not NULL, an additional filter, only packages on this list will be considered and their dependencies installed if needed (advanced usage only).
`dry`	(`logical`) dry run that outputs what would happen without actually doing it.
`verbose`	(`numeric`) verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)
`...`	Arguments passed on to `install_deps` `install_project` (`logical`) whether to also install the current package (i.e. the package named in `dependency_structure$current_pkg`), ignored unless `install_direction = "upstream"` (because downstream deps automatically install all their upstream deps) `install_direction` "upstream", "downstream" or "all"; which packages to install (according to dependency structure). By default this is only "upstream"

Value

data.frame of performed actions

Examples

## Not run: 
x <- dependency_table(project = ".", verbose = 1)

check_downstream(x, verbose = 1)
check_downstream(x, verbose = 1, only_test = TRUE, check_args = c("--no-manual"))

## End(Not run)
## Not run: 
x <- dependency_table(project = ".", verbose = 1)

check_downstream(x, verbose = 1)
check_downstream(x, verbose = 1, only_test = TRUE, check_args = c("--no-manual"))

## End(Not run)

Check & install downstream job

Description

Check & install downstream job

Usage

check_downstream_job(
  project = ".",
  verbose = 1,
  create_args = list(renv_profile = Sys.getenv("RENV_PROFILE")),
  ...
)
check_downstream_job(
  project = ".",
  verbose = 1,
  create_args = list(renv_profile = Sys.getenv("RENV_PROFILE")),
  ...
)

Arguments

`project`	(`character`) If `project_type` is `local` then directory of project (for which to calculate the dependency structure); must be a git repository. If `project_type` is `repo@host` then should be character of the form `⁠openpharma/stageddeps.food@https://github.com⁠` If host is not included in the string then the default `⁠https://github.com⁠` is assumed.
`verbose`	(`numeric`) verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)
`create_args`	`named list` - additional arguments passed to `dependency_table` function
`...`	Arguments passed on to `check_downstream` `distance` (`numeric`) additional filter to only install downstream packages at most this distance from the `dependency_structure$current_pkg` (advanced use only) `check_args` (`list`) arguments passed to `rcmdcheck` `only_tests` (`logical`) whether to only run tests (rather than checks) `dep_structure` (`dependency_structure`) output of function `dependency_table`; uses `dep_structure$table` to infer the packages to apply action to and infer installation order; uses `dep_structure$deps` to infer upstream dependencies `install_external_deps` logical to describe whether to install external dependencies of package using `remotes::install_deps()` (or `renv::install()` if inside an renv environment) . `upgrade` argument passed to `remotes::install_deps()`, defaults to `'never'`. Ignored if inside an `renv` environment. `package_list` (`character`) If not NULL, an additional filter, only packages on this list will be considered and their dependencies installed if needed (advanced usage only). `dry` (`logical`) dry run that outputs what would happen without actually doing it.

Examples

## Not run: 
check_downstream_job(check_args = Sys.getenv("RCMDCHECK_ARGS"))
check_downstream_job(
  check_args = Sys.getenv("RCMDCHECK_ARGS"),
  list(create_arg = list(ref = "6_makegraph@main"))
)
check_downstream_job(only_tests = TRUE)

## End(Not run)
## Not run: 
check_downstream_job(check_args = Sys.getenv("RCMDCHECK_ARGS"))
check_downstream_job(
  check_args = Sys.getenv("RCMDCHECK_ARGS"),
  list(create_arg = list(ref = "6_makegraph@main"))
)
check_downstream_job(only_tests = TRUE)

## End(Not run)

Checks that the staged dependency yamls are consistent with the dependencies listed in the DESCRIPTION files

Description

Checks that the staged dependency yamls are consistent with the dependencies listed in the DESCRIPTION files

Usage

check_yamls_consistent(dep_structure, skip_if_missing_yaml = FALSE)
check_yamls_consistent(dep_structure, skip_if_missing_yaml = FALSE)

Arguments

`dep_structure`	`dependency_structure` object
`skip_if_missing_yaml`	`logical` should checks be skipped on packages without yaml files. Default `FALSE`

Details

This function explicitly checks that for all packages in the dependency_structure object: all upstream and downstream packages specified in each yaml file are found in the appropriate package DESCRIPTION file

Value

NULL if successful. An error is thrown if inconsistencies found

Examples

## Not run: 
x <- dependency_table(project = ".")
check_yamls_consistent(x)

## End(Not run)
## Not run: 
x <- dependency_table(project = ".")
check_yamls_consistent(x)

## End(Not run)

Clear the repository cache

Description

Use this function to clear the package cache of some or all repositories (depending on pattern) if the git operations fail.

Usage

clear_cache(pattern = "*")
clear_cache(pattern = "*")

Arguments

pattern

files to remove, see unlink (wildcards * and ⁠?⁠ allowed)

Examples

## Not run: 
clear_cache()
clear_cache("*elecinfra*")

## End(Not run)
## Not run: 
clear_cache()
clear_cache("*elecinfra*")

## End(Not run)

Create dependency structure of your package collection

Description

Create dependency structure of your package collection

Usage

dependency_table(
  project = ".",
  project_type = c("local", "repo@host")[1],
  ref = NULL,
  local_repos = if ((project_type) == "local") get_local_pkgs_from_config() else NULL,
  direction = "all",
  fallback_branch = "main",
  renv_profile = NULL,
  verbose = 1
)
dependency_table(
  project = ".",
  project_type = c("local", "repo@host")[1],
  ref = NULL,
  local_repos = if ((project_type) == "local") get_local_pkgs_from_config() else NULL,
  direction = "all",
  fallback_branch = "main",
  renv_profile = NULL,
  verbose = 1
)

Arguments

`project`	(`character`) If `project_type` is `local` then directory of project (for which to calculate the dependency structure); must be a git repository. If `project_type` is `repo@host` then should be character of the form `⁠openpharma/stageddeps.food@https://github.com⁠` If host is not included in the string then the default `⁠https://github.com⁠` is assumed.
`project_type`	(`character`) See `project` argument.
`ref`	(`character`) git branch (or tag) inferred from the branch of the project if not provided; warning if not consistent with current branch of project. If `project_type` is not `local` then this argument must be provided.
`local_repos`	(`data.frame`) repositories that should be taken from local file system rather than cloned; columns are `⁠repo, host, directory⁠`.
`direction`	(`character`) direction in which to discover packages either "upstream","downstream" or "all".
`fallback_branch`	(`character`) the default branch to try to use if no other matches found. It defaults to `"main"`.
`renv_profile`	(`character`) the name of the renv profile of the `renv.lock` files to be included from the repos. The standard `renv.lock` file uses the default `NULL` argument here.
`verbose`	(`numeric`) verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)

Value

dependency_structure An S3 object with the following items:

project: project argument used to create the object (absolute path if project_type is local
project_type: project_type used to create object
current_pkg: The R package name of code in the project directory
table: data.frame contain one row per r package discovered, with the following rows package_name, type (current, upstream, downstream or other), distance (minimum number of steps from current_pkg), ref, repo, host, sha cache_dir, accessible, installable and install_index (the order to install the packages). Note some items are are suppressed when printing the object
deps: list with three elements, upstream_depsis the graph where edges point from a package to its upstream dependencies. They are ordered in installation order. The downstream_deps list is the graph with the edge direction flipped, and is ordered in reverse installation order. external contains the external R packages found in the description files of the internal packages. It is a dataframe of the form returned by desc::desc_get_deps
direction: direction argument used to create object
renv_files: ⁠named list⁠ containing the json of the renv.lock files for the chosen profile for each repo. An entry to the list is NULL if a repos does not have the required lock file

Examples

## Not run: 
dependency_table(verbose = 1)
dependency_table(
  project = "openpharma/stageddeps.food@https://github.com",
  project_type = "repo@host",
  ref = "main"
)
x <- dependency_table(
  project = "path/to/project",
  direction = c("upstream")
)
print(x)
plot(x)

## End(Not run)
## Not run: 
dependency_table(verbose = 1)
dependency_table(
  project = "openpharma/stageddeps.food@https://github.com",
  project_type = "repo@host",
  ref = "main"
)
x <- dependency_table(
  project = "path/to/project",
  direction = c("upstream")
)
print(x)
plot(x)

## End(Not run)

Determine the branch/tag to install based on feature (staging rules)

Description

Return the git ref (tag or branch) of the repo to install given the available branches and tags.

Usage

determine_ref(ref, available_refs, fallback_branch = "main", branch_sep = "@")
determine_ref(ref, available_refs, fallback_branch = "main", branch_sep = "@")

Arguments

`ref`	ref we want to build
`available_refs`	data.frame with columns `ref` the names of the available refs and `type` (`branch` or `tag`)
`fallback_branch`	the default branch to try to use if no other matches found
`branch_sep`	separator between branches in `feature`, `/` does not work well with `git` because it clashes with the filesystem paths

Details

A ref is either a tag or branches separated by slashes of the form name1@name2@...@nameN. Where separator is specified by branch_sep argument

This function checks for an exact match for the tag if this is not found then among the available branches, it searches in the order name1@name2@...@nameN, name2@name3@...@nameN, name3@name4@...@nameN, ..., nameN

Value

branch/tag to choose to match feature, error if no suitable branch was provided with the type attribute "tag" or "branch"

Examples

determine_ref(
  "feature1",
  data.frame(ref = c("main", "feature1"), type = "branch")
) == structure("feature1", type = "branch")

determine_ref(
  "feature1@devel",
  data.frame(ref = c("main", "devel", "feature1"), type = "branch")
) == structure("devel", type = "branch")

determine_ref(
  ref = "fix1@feature1@devel",
  available_refs = data.frame(
    ref = c(
      "main", "devel", "feature1", "feature1@devel",
      "fix1@feature1@devel", "fix1"
    ),
    type = "branch"
  )
) == structure("fix1@feature1@devel", type = "branch")

determine_ref(
  "fix1@feature1@devel",
  data.frame(
    ref = c("main", "devel", "feature1", "feature1@devel", "fix1"),
    type = "branch"
  )
) == structure("feature1@devel", type = "branch")

determine_ref(
  "fix1@feature1@devel",
  data.frame(ref = c("main", "devel", "feature1", "fix1"), type = "branch")
) == structure("devel", type = "branch")

determine_ref("feature1@release", data.frame(ref = c("main", "devel"), type = "branch"))

# error because neither `feature1@release` nor `release` branch exists
# determine_ref("feature1@release", data.frame(ref = c("master", "devel"), type = "branch"))

# tag examples
determine_ref(
  "v0.1",
  data.frame(ref = c("main", "devel", "feature1", "v0.1"), type = c(rep("branch", 3), "tag"))
) == structure("v0.1", type = "tag")

determine_ref(
  "v0.2",
  data.frame(ref = c("main", "devel", "feature1", "v0.1"), type = c(rep("branch", 3), "tag"))
) == structure("main", type = "branch")

determine_ref(
  "feature1",
  data.frame(ref = c("main", "feature1"), type = "branch")
) == structure("feature1", type = "branch")

determine_ref(
  "feature1@devel",
  data.frame(ref = c("main", "devel", "feature1"), type = "branch")
) == structure("devel", type = "branch")

determine_ref(
  ref = "fix1@feature1@devel",
  available_refs = data.frame(
    ref = c(
      "main", "devel", "feature1", "feature1@devel",
      "fix1@feature1@devel", "fix1"
    ),
    type = "branch"
  )
) == structure("fix1@feature1@devel", type = "branch")

determine_ref(
  "fix1@feature1@devel",
  data.frame(
    ref = c("main", "devel", "feature1", "feature1@devel", "fix1"),
    type = "branch"
  )
) == structure("feature1@devel", type = "branch")

determine_ref(
  "fix1@feature1@devel",
  data.frame(ref = c("main", "devel", "feature1", "fix1"), type = "branch")
) == structure("devel", type = "branch")

determine_ref("feature1@release", data.frame(ref = c("main", "devel"), type = "branch"))

# error because neither `feature1@release` nor `release` branch exists
# determine_ref("feature1@release", data.frame(ref = c("master", "devel"), type = "branch"))

# tag examples
determine_ref(
  "v0.1",
  data.frame(ref = c("main", "devel", "feature1", "v0.1"), type = c(rep("branch", 3), "tag"))
) == structure("v0.1", type = "tag")

determine_ref(
  "v0.2",
  data.frame(ref = c("main", "devel", "feature1", "v0.1"), type = c(rep("branch", 3), "tag"))
) == structure("main", type = "branch")

List the external R packages required to be installed

Description

List the external R packages required to be installed

Usage

get_all_external_dependencies(
  dep_structure,
  available_packages = as.data.frame(utils::available.packages()),
  install_direction = "upstream",
  package_list = NULL,
  from_internal_dependencies = c("Depends", "Imports", "LinkingTo", "Suggests"),
  from_external_dependencies = c("Depends", "Imports", "LinkingTo")
)
get_all_external_dependencies(
  dep_structure,
  available_packages = as.data.frame(utils::available.packages()),
  install_direction = "upstream",
  package_list = NULL,
  from_internal_dependencies = c("Depends", "Imports", "LinkingTo", "Suggests"),
  from_external_dependencies = c("Depends", "Imports", "LinkingTo")
)

Arguments

`dep_structure`	(`dependency_structure`) output of function `dependency_table`; uses `dep_structure$table` to infer the packages to apply action to and infer installation order; uses `dep_structure$deps` to infer upstream dependencies
`available_packages`	(`data.frame`) A dataframe of the format given by `as.data.frame(utils::available.packages)`. It is unlikely this default needs to be changed; however you need to ensure the `options("repos")` contains the urls of all expected repos (e.g. Bioconductor).
`install_direction`	"upstream", "downstream" or "all"; which packages to install (according to dependency structure). By default this is only "upstream"
`package_list`	(`character`) If not NULL, an additional filter, only packages on this list will be considered and their dependencies installed if needed (advanced usage only).
`from_internal_dependencies`	Vector chosen from `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")` which fields of the DESCRIPTION file of the internal packages should be included. Default: `c("Depends", "Imports", "LinkingTo", "Suggests")`
`from_external_dependencies`	Vector chosen from `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")` which fields of the DESCRIPTION file of the internal packages should be included. Default: `c("Depends", "Imports", "LinkingTo")`

Value

A vector of 'external' R packages required to install the selected 'internal' packages, ordered by install order (unless from_external_dependencies does not include "Depends", "Imports" and "LinkingTo"). The core R packages (e.g. methods, utils) are not included. The output can be used with remotes::system_requirements to extract the system requirements needed for your packages, see example below.

Examples

## Not run: 
x <- dependency_table("openpharma/stageddeps.electricity",
  project_type = "repo@host", feature = "main"
)

# get external package dependencies
ex_deps <- get_all_external_dependencies(x)
print(ex_deps)

# get system dependencies (in this case there are none)
unique(unlist(lapply(ex_deps,
  function(pkg, ...) {
    remotes::system_requirements(package = pkg, ...)
  },
  os = "ubuntu",
  os_release = "20.04"
)))

## End(Not run)
## Not run: 
x <- dependency_table("openpharma/stageddeps.electricity",
  project_type = "repo@host", feature = "main"
)

# get external package dependencies
ex_deps <- get_all_external_dependencies(x)
print(ex_deps)

# get system dependencies (in this case there are none)
unique(unlist(lapply(ex_deps,
  function(pkg, ...) {
    remotes::system_requirements(package = pkg, ...)
  },
  os = "ubuntu",
  os_release = "20.04"
)))

## End(Not run)

Loads the config file and extracts `local_packages`

Description

Checks that all directories exist and are absolute paths.

Usage

get_local_pkgs_from_config()
get_local_pkgs_from_config()

Value

local_packages

Examples

get_local_pkgs_from_config()
get_local_pkgs_from_config()

Install dependencies of project

Description

Given a dependency_structure object, install the R packages

Usage

install_deps(
  dep_structure,
  install_project = TRUE,
  install_direction = "upstream",
  install_external_deps = TRUE,
  upgrade = "never",
  package_list = NULL,
  dry = FALSE,
  verbose = 1,
  ...
)
install_deps(
  dep_structure,
  install_project = TRUE,
  install_direction = "upstream",
  install_external_deps = TRUE,
  upgrade = "never",
  package_list = NULL,
  dry = FALSE,
  verbose = 1,
  ...
)

Arguments

`dep_structure`	(`dependency_structure`) output of function `dependency_table`; uses `dep_structure$table` to infer the packages to apply action to and infer installation order; uses `dep_structure$deps` to infer upstream dependencies
`install_project`	(`logical`) whether to also install the current package (i.e. the package named in `dependency_structure$current_pkg`), ignored unless `install_direction = "upstream"` (because downstream deps automatically install all their upstream deps)
`install_direction`	"upstream", "downstream" or "all"; which packages to install (according to dependency structure). By default this is only "upstream"
`install_external_deps`	logical to describe whether to install external dependencies of package using `remotes::install_deps()` (or `renv::install()` if inside an renv environment) .
`upgrade`	argument passed to `remotes::install_deps()`, defaults to `'never'`. Ignored if inside an `renv` environment.
`package_list`	(`character`) If not NULL, an additional filter, only packages on this list will be considered and their dependencies installed if needed (advanced usage only).
`dry`	(`logical`) dry run that outputs what would happen without actually doing it.
`verbose`	(`numeric`) verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)
`...`	Additional args passed to `remotes::install_deps()`. Ignored if inside an `renv` environment.

Value

data.frame of performed actions

Examples

## Not run: 
x <- dependency_table(project = "./path/to/project")

install_deps(x)

# install all dependencies
install_deps(x, install_direction = "all")

## End(Not run)
## Not run: 
x <- dependency_table(project = "./path/to/project")

install_deps(x)

# install all dependencies
install_deps(x, install_direction = "all")

## End(Not run)

Gadget or Shiny app to select the dependencies to install

Description

The dependencies are obtained by traversing the upstream and downstream repositories in the package's staged dependencies yaml files starting from project.

Usage

install_deps_app(
  default_repo = NULL,
  default_host = "https://github.com",
  default_ref = "main",
  fallback_branch = "main",
  run_gadget = TRUE,
  run_as_job = TRUE,
  verbose = 1,
  install_external_deps = TRUE,
  renv_profile = NULL,
  upgrade = "never",
  ...
)
install_deps_app(
  default_repo = NULL,
  default_host = "https://github.com",
  default_ref = "main",
  fallback_branch = "main",
  run_gadget = TRUE,
  run_as_job = TRUE,
  verbose = 1,
  install_external_deps = TRUE,
  renv_profile = NULL,
  upgrade = "never",
  ...
)

Arguments

`default_repo`	(`character`) the repository name for the dependency graph to be created for, for example, `"openpharma/stageddeps.water"`. If `NULL` this must be entered by app user and can always be changed by the user.
`default_host`	(`character`) the host for the repository for the dependency graph to be created for by default `"https://github.com"`. If `NULL` this must be entered by app user and can always be changed by the user.
`default_ref`	(`character`) default ref (branch/tag), see also the parameter `ref` of `⁠\link{dependency_table}⁠`. If `NULL` this must be entered by app user and can always be changed by the user.
`fallback_branch`	(`character`) the default branch to try to use if no other matches found
`run_gadget`	(`logical`) whether to run the app as a gadget
`run_as_job`	(`logical`) whether to run the installation as an RStudio job.
`verbose`	(`numeric`) verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)
`install_external_deps`	logical to describe whether to install external dependencies of package using `remotes::install_deps()` (or `renv::install()` if inside an renv environment) .
`renv_profile`	(`character`) the name of the `renv` profile of the `renv.lock` files to be included from the repos. The standard `renv.lock` file uses the default `NULL` argument here.
`upgrade`	argument passed to `remotes::install_deps()`, defaults to `'never'`. Ignored if inside an `renv` environment.
`...`	Additional args passed to `remotes::install_deps()`. Ignored if inside an `renv` environment.

Value

shiny.app or value returned by app (executed as a gadget)

Examples

## Not run: 
install_deps_app("openpharma/stageddeps.food")

## End(Not run)
## Not run: 
install_deps_app("openpharma/stageddeps.food")

## End(Not run)

Install dependencies job

Description

Install dependencies job

Usage

install_deps_job(
  project = ".",
  project_type = "local",
  verbose = 1,
  create_args = list(renv_profile = Sys.getenv("RENV_PROFILE")),
  ...
)
install_deps_job(
  project = ".",
  project_type = "local",
  verbose = 1,
  create_args = list(renv_profile = Sys.getenv("RENV_PROFILE")),
  ...
)

Arguments

`project`	(`character`) If `project_type` is `local` then directory of project (for which to calculate the dependency structure); must be a git repository. If `project_type` is `repo@host` then should be character of the form `⁠openpharma/stageddeps.food@https://github.com⁠` If host is not included in the string then the default `⁠https://github.com⁠` is assumed.
`project_type`	(`character`) See `project` argument.
`verbose`	(`numeric`) verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)
`create_args`	`named list` - additional arguments passed to `dependency_table` function
`...`	Arguments passed on to `install_deps` `dep_structure` (`dependency_structure`) output of function `dependency_table`; uses `dep_structure$table` to infer the packages to apply action to and infer installation order; uses `dep_structure$deps` to infer upstream dependencies `install_project` (`logical`) whether to also install the current package (i.e. the package named in `dependency_structure$current_pkg`), ignored unless `install_direction = "upstream"` (because downstream deps automatically install all their upstream deps) `install_direction` "upstream", "downstream" or "all"; which packages to install (according to dependency structure). By default this is only "upstream" `install_external_deps` logical to describe whether to install external dependencies of package using `remotes::install_deps()` (or `renv::install()` if inside an renv environment) . `upgrade` argument passed to `remotes::install_deps()`, defaults to `'never'`. Ignored if inside an `renv` environment. `package_list` (`character`) If not NULL, an additional filter, only packages on this list will be considered and their dependencies installed if needed (advanced usage only). `dry` (`logical`) dry run that outputs what would happen without actually doing it.

Examples

## Not run: 
install_deps_job()
install_deps_job(create_args = list(ref = "6_makegraph@main"))

# install all dependencies
install_deps_job(create_args = list(direction = "all"))
install_deps_job(dry_install = TRUE)

## End(Not run)
## Not run: 
install_deps_job()
install_deps_job(create_args = list(ref = "6_makegraph@main"))

# install all dependencies
install_deps_job(create_args = list(direction = "all"))
install_deps_job(dry_install = TRUE)

## End(Not run)

Install a git repository

Description

It adds the git SHA to the DESCRIPTION file, so that the package does not need to be installed again when the same commit is already installed.

Usage

install_repo_add_sha(repo_dir, ...)
install_repo_add_sha(repo_dir, ...)

Arguments

`repo_dir`	directory of repo
`...`	Additional args passed to `remotes::install_deps`. Note `upgrade` is set to "never" and shouldn't be passed into this function.

Topological graph sort

Description

Graph is a list which for each node contains a vector of child nodes in the returned list, parents appear before their children.

Usage

topological_sort(graph)
topological_sort(graph)

Arguments

graph

(named list) list with node vector elements mapping from child to its parents (upstream dependencies)

Details

Implementation of Kahn algorithm with a modification to maintain the order of input elements.

Value

vector listing parents before children

Examples

staged.dependencies:::topological_sort(list(A = c(), B = c("A"), C = c("B"), D = c("A")))
staged.dependencies:::topological_sort(list(D = c("A"), A = c(), B = c("A"), C = c("B")))
staged.dependencies:::topological_sort(list(D = c("A"), B = c("A"), C = c("B"), A = c()))
## Not run: 
# cycle
topological_sort(list(A = c("B"), B = c("C", "A"), C = c()))

## End(Not run)
staged.dependencies:::topological_sort(list(A = c(), B = c("A"), C = c("B"), D = c("A")))
staged.dependencies:::topological_sort(list(D = c("A"), A = c(), B = c("A"), C = c("B")))
staged.dependencies:::topological_sort(list(D = c("A"), B = c("A"), C = c("B"), A = c()))
## Not run: 
# cycle
topological_sort(list(A = c("B"), B = c("C", "A"), C = c()))

## End(Not run)

Update existing stage_dependencies yaml file

Description

Using the existing stage_dependencies yaml file 'graph' to define internal dependencies, update the project yaml file to include to include all direct (i.e. distance 1) upstream and downstream repos

Usage

update_with_direct_deps(dep_structure)
update_with_direct_deps(dep_structure)

Arguments

dep_structure

dep_structure object, output of dependency_table function with project_type = "local"

Set staged.dependencies verbosity

Description

Functions to set and remove the option parameter verbose_level_staged.deps. It can assume integer values between c(0, 1, 2). This will set this variable as an option with options() and getOption().

Usage

verbose_sd_set(verbose = 1)

verbose_sd_get()

verbose_sd_rm()
verbose_sd_set(verbose = 1)

verbose_sd_get()

verbose_sd_rm()

Arguments

verbose

(numeric)
verbosity level, incremental; (0: None, 1: packages that get installed + high-level git operations, 2: includes git checkout infos)

Examples

verbose_sd_set(2)
verbose_sd_get() # 2, the inserted value
verbose_sd_rm()
verbose_sd_get() # 1, the default

verbose_sd_set(2)
verbose_sd_get() # 2, the inserted value
verbose_sd_rm()
verbose_sd_get() # 1, the default

Package 'staged.dependencies'

Help Index

Build, check and install internal dependencies

Description

Usage

Arguments

Value

Examples

Check & install downstream dependencies

Description

Usage

Arguments

Value

Examples

Check & install downstream job

Description

Usage

Arguments

See Also

Examples

Checks that the staged dependency yamls are consistent with the dependencies listed in the DESCRIPTION files

Description

Usage

Arguments

Details

Value

Examples

Clear the repository cache

Description

Usage

Arguments

Examples

Create dependency structure of your package collection

Description

Usage

Arguments

Value

Examples

Determine the branch/tag to install based on feature (staging rules)

Description

Usage

Arguments

Details

Value

Examples

List the external R packages required to be installed

Description

Usage

Arguments

Value

Examples

Loads the config file and extracts local_packages

Description

Usage

Value

Examples

Install dependencies of project

Description

Usage

Arguments

Value

See Also

Examples

Gadget or Shiny app to select the dependencies to install

Description

Usage

Arguments

Value

Examples

Install dependencies job

Description

Usage

Arguments

See Also

Examples

Install a git repository

Description

Usage

Arguments

Topological graph sort

Loads the config file and extracts `local_packages`