Title:	Deal with Dependencies
Version:	0.4.5
Description:	Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2' documentation of functions. There is a function to update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.
License:	GPL-3
URL:	https://thinkr-open.github.io/attachment/, https://github.com/ThinkR-open/attachment
BugReports:	https://github.com/ThinkR-open/attachment/issues
VignetteBuilder:	knitr
Config/fusen/version:	0.6.0
Config/Needs/website:	ThinkR-open/thinkrtemplate
Config/testthat/edition:	3
Encoding:	UTF-8
RoxygenNote:	7.3.2
Language:	en-US
Depends:	R (≥ 3.4)
Imports:	cli, desc (≥ 1.2.0), glue (≥ 1.3.0), knitr (≥ 1.20), magrittr (≥ 1.5), rmarkdown (≥ 1.10), roxygen2, stats, stringr (≥ 1.3.1), utils, withr, yaml
Suggests:	lifecycle, renv (≥ 0.8.4), rstudioapi, testthat (≥ 3.0.0)
NeedsCompilation:	no
Packaged:	2025-03-14 17:54:04 UTC; PC
Author:	Vincent Guyader [cre, aut], Sébastien Rochette [aut] (previous maintainer), Murielle Delmotte [aut], Swann Floc'hlay [aut], ThinkR [cph, fnd]
Maintainer:	Vincent Guyader <vincent@thinkr.fr>
Repository:	CRAN
Date/Publication:	2025-03-14 20:30:01 UTC

attachment: Deal with Dependencies

Description

Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2' documentation of functions. There is a function to update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.

Author(s)

Maintainer: Vincent Guyader vincent@thinkr.fr (ORCID)

Authors:

• Sébastien Rochette sebastienrochettefr@gmail.com (ORCID) (previous maintainer)

• Murielle Delmotte murielle@thinkr.fr (ORCID)

• Swann Floc'hlay swann@thinkr.fr (ORCID)

Other contributors:

• ThinkR [copyright holder, funder]

See Also

Useful links:

• https://thinkr-open.github.io/attachment/

• https://github.com/ThinkR-open/attachment

• Report bugs at https://github.com/ThinkR-open/attachment/issues

Pipe operator

Description

See ⁠magrittr::[\%>\%][magrittr::pipe]⁠ for details.

Usage

lhs %>% rhs

Arguments

Value

The result of calling rhs(lhs).

Amend DESCRIPTION with dependencies read from package code parsing

Description

Amend package DESCRIPTION file with the list of dependencies extracted from R, examples, tests, vignettes files. att_to_desc_from_pkg() is an alias of att_amend_desc(), for the correspondence with att_to_desc_from_is().

Usage

att_amend_desc(
  path = ".",
  path.n = "NAMESPACE",
  path.d = "DESCRIPTION",
  dir.r = "R",
  dir.v = "vignettes",
  dir.t = "tests",
  extra.suggests = NULL,
  pkg_ignore = NULL,
  document = TRUE,
  normalize = TRUE,
  inside_rmd = FALSE,
  must.exist = TRUE,
  check_if_suggests_is_installed = TRUE,
  update.config = FALSE,
  use.config = TRUE,
  path.c = "dev/config_attachment.yaml"
)

att_to_desc_from_pkg(
  path = ".",
  path.n = "NAMESPACE",
  path.d = "DESCRIPTION",
  dir.r = "R",
  dir.v = "vignettes",
  dir.t = "tests",
  extra.suggests = NULL,
  pkg_ignore = NULL,
  document = TRUE,
  normalize = TRUE,
  inside_rmd = FALSE,
  must.exist = TRUE,
  check_if_suggests_is_installed = TRUE,
  update.config = FALSE,
  use.config = TRUE,
  path.c = "dev/config_attachment.yaml"
)

Arguments

Details

Your daily use is to run att_amend_desc(), as is. You will want to run this function sometimes with some extra information like att_amend_desc(pkg_ignore = "x", update.config = TRUE) if you have to update the configuration file. Next time att_amend_desc() will use these parameters from the configuration file directly.

Value

Update DESCRIPTION file.

Examples

# Run on an external "dummypackage" as an example
# For your local use, you do not have to specify the `path` as below
# By default, `att_amend_desc()` will run on the current working directory

# Create a fake package for the example
tmpdir <- tempfile(pattern = "description")
dir.create(tmpdir)
file.copy(system.file("dummypackage",package = "attachment"), tmpdir,
 recursive = TRUE)
dummypackage <- file.path(tmpdir, "dummypackage")

# Update documentation and dependencies
att_amend_desc(path = dummypackage)

# You can look at the content of this external package
#' # browseURL(dummypackage)

# Update the config file with extra parameters
# We recommend that you store this code in a file in your "dev/" directory
# to run it when needed
att_amend_desc(path = dummypackage, extra.suggests = "testthat", update.config = TRUE)

# Next time, in your daily development
att_amend_desc(path = dummypackage)

# Clean after examples
unlink(tmpdir, recursive = TRUE)

Look for functions called in data loading code

Description

Look for functions called in data loading code

Usage

att_from_data(chr)

Arguments

Value

A character vector containing the names of the packages from which datasets are being loaded.

Examples

vec_char <- 'data("starwars", package = "dplyr")'
att_from_data(vec_char)

Return all package dependencies from current package

Description

Return all package dependencies from current package

Usage

att_from_description(
  path = "DESCRIPTION",
  dput = FALSE,
  field = c("Depends", "Imports", "Suggests")
)

Arguments

Value

A character vector with packages names

Examples

dummypackage <- system.file("dummypackage", package = "attachment")
# browseURL(dummypackage)
att_from_description(path = file.path(dummypackage, "DESCRIPTION"))

Get all packages called in examples from R files

Description

Get all packages called in examples from R files

Usage

att_from_examples(dir.r = "R")

Arguments

Value

Character vector of packages called with library or require.

Examples

dummypackage <- system.file("dummypackage",package = "attachment")

# browseURL(dummypackage)
att_from_examples(dir.r = file.path(dummypackage,"R"))

return package dependencies from NAMESPACE file

Description

return package dependencies from NAMESPACE file

Usage

att_from_namespace(path = "NAMESPACE", document = TRUE, clean = TRUE)

Arguments

Value

a vector

Examples

tmpdir <- tempfile(pattern = "namespace")
dir.create(tmpdir)
file.copy(system.file("dummypackage",package = "attachment"), tmpdir,
 recursive = TRUE)
dummypackage <- file.path(tmpdir, "dummypackage")
# browseURL(dummypackage)
att_from_namespace(path = file.path(dummypackage, "NAMESPACE"))

# Clean temp files after this example
unlink(tmpdir, recursive = TRUE)

Get all dependencies from a Rmd file

Description

Get all dependencies from a Rmd file

Usage

att_from_rmd(
  path,
  temp_dir = tempdir(),
  warn = -1,
  encoding = getOption("encoding"),
  inside_rmd = FALSE,
  inline = TRUE
)

att_from_qmd(
  path,
  temp_dir = tempdir(),
  warn = -1,
  encoding = getOption("encoding"),
  inside_rmd = FALSE,
  inline = TRUE
)

Arguments

Value

vector of character of packages names found in the Rmd

Examples

dummypackage <- system.file("dummypackage",package = "attachment")
# browseURL(dummypackage)
att_from_rmd(path = file.path(dummypackage,"vignettes/demo.Rmd"))

Get all packages called in vignettes folder

Description

Get all packages called in vignettes folder

Usage

att_from_rmds(
  path = "vignettes",
  pattern = "*.[.](Rmd|rmd|qmd)$",
  recursive = TRUE,
  warn = -1,
  inside_rmd = FALSE,
  inline = TRUE,
  folder_to_exclude = "renv"
)

att_from_qmds(
  path = "vignettes",
  pattern = "*.[.](Rmd|rmd|qmd)$",
  recursive = TRUE,
  warn = -1,
  inside_rmd = FALSE,
  inline = TRUE,
  folder_to_exclude = "renv"
)

Arguments

Value

Character vector of packages called with library or require. knitr and rmarkdown are added by default to allow building the vignettes if the directory contains "vignettes" in the path

Examples

dummypackage <- system.file("dummypackage",package = "attachment")
# browseURL(dummypackage)
att_from_rmds(path = file.path(dummypackage,"vignettes"))

Look for functions called with :: and library/requires in one script

Description

Look for functions called with :: and library/requires in one script

Usage

att_from_rscript(path)

Arguments

Details

Calls from pkg::fun in roxygen skeleton and comments are ignored

Value

a vector

Examples

dummypackage <- system.file("dummypackage",package = "attachment")
# browseURL(dummypackage)

att_from_rscript(path = file.path(dummypackage,"R","my_mean.R"))

Look for functions called with :: and library/requires in folder of scripts

Description

Look for functions called with :: and library/requires in folder of scripts

Usage

att_from_rscripts(
  path = "R",
  pattern = "*.[.](r|R)$",
  recursive = TRUE,
  folder_to_exclude = "renv"
)

Arguments

Value

vector of character of packages names found in the R script

Examples

dummypackage <- system.file("dummypackage",package = "attachment")
# browseURL(dummypackage)

att_from_rscripts(path = file.path(dummypackage, "R"))
att_from_rscripts(path = list.files(file.path(dummypackage, "R"), full.names = TRUE))

Amend DESCRIPTION with dependencies from imports and suggests package list

Description

Amend DESCRIPTION with dependencies from imports and suggests package list

Usage

att_to_desc_from_is(
  path.d = "DESCRIPTION",
  imports = NULL,
  suggests = NULL,
  check_if_suggests_is_installed = TRUE,
  normalize = TRUE,
  must.exist = TRUE
)

Arguments

Details

must.exist is better set to TRUE during package development. This stops the process when a package does not exists on your system. This avoids check errors with typos in package names in DESCRIPTION. When used in CI to discover dependencies, for a bookdown for instance, you may want to set to FALSE (no message at all) or NA (warning for not installed).

Value

Fill in Description file

Examples

tmpdir <- tempfile(pattern = "descfromis")
dir.create(tmpdir)
file.copy(system.file("dummypackage",package = "attachment"), tmpdir,
 recursive = TRUE)
dummypackage <- file.path(tmpdir, "dummypackage")
# browseURL(dummypackage)
att_to_desc_from_is(path.d = file.path(dummypackage, "DESCRIPTION"),
imports = c("magrittr", "attachment"), suggests = c("knitr"))

# In combination with other functions
att_to_desc_from_is(path.d = file.path(dummypackage, "DESCRIPTION"),
imports = att_from_rscripts(file.path(dummypackage, "R")),
suggests = att_from_rmds(file.path(dummypackage, "vignettes")))

# Clean temp files after this example
unlink(tmpdir, recursive = TRUE)

Deprecated functions

Description

List of functions deprecated. They will be removed in a future release.

Usage

att_to_description(
  path = ".",
  path.n = "NAMESPACE",
  path.d = "DESCRIPTION",
  dir.r = "R",
  dir.v = "vignettes",
  dir.t = "tests",
  extra.suggests = NULL,
  pkg_ignore = NULL,
  document = TRUE,
  normalize = TRUE,
  inside_rmd = FALSE
)

Arguments

Value

List of functions used for deprecation side effects. Output depends on the deprecated function.

Details

Construct a Remote Branch Reference String

Description

This function constructs a reference string for a remote branch in a version control system like Git. It returns a formatted string combining the remote name and a specified branch or reference.

Usage

complete_remote_branch(remote, remoteref = "HEAD")

Arguments

Value

A character string. If remoteref is "HEAD", it returns just the remote string. If remoteref is not "HEAD", it returns a string in the format "remote@remoteref".

Create the list of instructions to install dependencies from a DESCRIPTION file

Description

Outputs the list of instructions and a "dependencies.R" file with instructions in the "inst/" directory

Usage

create_dependencies_file(
  path = "DESCRIPTION",
  field = c("Depends", "Imports"),
  to = "inst/dependencies.R",
  open_file = TRUE,
  ignore_base = TRUE,
  install_only_if_missing = FALSE
)

Arguments

Value

List of R instructions to install all dependencies from a DESCRIPTION file. Side effect: creates a R file containing these instructions.

Examples

# Create a fake package
tmpdir <- tempfile(pattern = "depsfile")
dir.create(tmpdir)
file.copy(system.file("dummypackage",package = "attachment"), tmpdir,
          recursive = TRUE)
dummypackage <- file.path(tmpdir, "dummypackage")

# Create the dependencies commands but no file
create_dependencies_file(
  path = file.path(dummypackage,"DESCRIPTION"),
  to = NULL,
  open_file = FALSE)

# Create the dependencies files in the package
create_dependencies_file(
  path = file.path(dummypackage,"DESCRIPTION"),
  to = file.path(dummypackage, "inst/dependencies.R"),
  open_file = FALSE)
list.files(file.path(dummypackage, "inst"))
# browseURL(dummypackage)

# Clean temp files after this example
unlink(tmpdir, recursive = TRUE)

Create reproducible environments for your R projects with renv

Description

Tool to create and maintain renv.lock files. The idea is to have 2 distinct files, one for development and the other for deployment. Indeed, although packages like attachment or pkgload must be installed to develop, they are not necessary in your project, package or Shiny application.

Usage

create_renv_for_dev(
  path = ".",
  dev_pkg = "_default",
  folder_to_include = c("dev", "data-raw", "renv"),
  folder_to_exclude = c("renv"),
  output = "renv.lock",
  install_if_missing = TRUE,
  document = TRUE,
  pkg_ignore = NULL,
  check_if_suggests_is_installed = TRUE,
  ...
)

create_renv_for_prod(
  path = ".",
  output = "renv.lock.prod",
  dev_pkg = "remotes",
  check_if_suggests_is_installed = FALSE,
  ...
)

Arguments

Value

a renv.lock file

Examples

## Not run: 
# Writes a renv.lock a file in the user directory
create_renv_for_dev()
create_renv_for_dev(dev_pkg = "attachment")
create_renv_for_prod()

## End(Not run)

Proposes values for Remotes field for DESCRIPTION file based on your installation

Description

Proposes values for Remotes field for DESCRIPTION file based on your installation

Usage

find_remotes(pkg)

Arguments

Value

List of all non-CRAN packages and code to add in Remotes field in DESCRIPTION. NULL otherwise.

Examples

# Find from vector of packages
find_remotes(pkg = c("attachment", "desc", "glue"))

# Find from Description file
dummypackage <- system.file("dummypackage", package = "attachment")
att_from_description(
path = file.path(dummypackage, "DESCRIPTION")) %>%
find_remotes()

## Not run: 
# For the current package directory
att_from_description() %>% find_remotes()

## End(Not run)


# For a specific package name
find_remotes("attachment")

# Find remotes from all installed packages
find_remotes(list.dirs(.libPaths(), full.names = FALSE, recursive = FALSE))

Install missing package from DESCRIPTION

Description

Install missing package from DESCRIPTION

Usage

install_from_description(
  path = "DESCRIPTION",
  field = c("Depends", "Imports", "Suggests"),
  ...
)

Arguments

Value

Used for side effect. Installs R packages from DESCRIPTION file if missing.

Examples

## Not run: 
# This will install packages on your system
dummypackage <- system.file("dummypackage", package = "attachment")
# browseURL(dummypackage)

install_from_description(path = file.path(dummypackage, "DESCRIPTION"))

## End(Not run)

install packages if missing

Description

install packages if missing

Usage

install_if_missing(to_be_installed, ...)

Arguments

Value

Used for side effect. Install missing packages from the character vector input.

Examples

## Not run: 
# This will install packages on your system
install_if_missing(c("dplyr", "fcuk", "rusk"))

## End(Not run)

Add Remotes field to DESCRIPTION based on your local installation

Description

Add Remotes field to DESCRIPTION based on your local installation

Usage

set_remotes_to_desc(path.d = "DESCRIPTION", stop.local = FALSE, clean = TRUE)

Arguments

Value

Used for side effect. Adds Remotes field in DESCRIPTION file.

Examples

tmpdir <- tempfile(pattern = "setremotes")
dir.create(tmpdir)
file.copy(system.file("dummypackage", package = "attachment"), tmpdir,
 recursive = TRUE)
dummypackage <- file.path(tmpdir, "dummypackage")
# Add remotes field if there are Remotes locally
att_amend_desc(dummypackage) %>%
  set_remotes_to_desc()

# Clean temp files after this example
unlink(tmpdir, recursive = TRUE)

## Not run: 
# For your current package
att_amend_desc() %>%
  set_remotes_to_desc()

## End(Not run)