attachment 
The goal of attachment is to help to deal with package dependencies during package development. It also gives useful tools to install or list missing packages used inside Rscripts or Rmds.
When building a package, we have to add @importFrom in our
documentation or pkg::fun in the R code. The most important is not to
forget to add the list of dependencies in the βImportsβ or βSuggestsβ
package lists in the DESCRIPTION file.
Why do you have to repeat twice the same thing ?
And what happens when you remove a dependency for one of your functions
? Do you really want to run a βFind in filesβ to verify that you do not
need this package anymore ?
Let {attachment} help you ! This reads your NAMESPACE, your functions in R directory and your vignettes, then update the DESCRIPTION file accordingly. Are you ready to be lazy ?
See full documentation realized using {pkgdown} at https://thinkr-open.github.io/attachment/
Installation
CRAN version
install.packages("attachment")Development version
install.packages('attachment', repos = c('https://thinkr-open.r-universe.dev', 'https://cloud.r-project.org'))Declare all dependencies in DESCRIPTION during package development
What you really want is to fill and update your description file along with the modifications of your documentation. Indeed, only the following function will really be called. Use and abuse during the development of your package !
attachment::att_amend_desc(){attachment} detects all calls to library(pkg), @importFrom pkg fun,
pkg::fun() in the different classical directories of your R package,
then list them in the correct βImportsβ or βSuggestsβ category in the
DESCRIPTION file, according to their position in the package.
Declare extra dependencies for extra uses
If you want to add extra packages like {pkgdown} or {covr} that are not listed in any script in your package, a call for your development packages would be:
attachment::att_amend_desc(extra.suggests = c("pkgdown", "covr"), update.config = TRUE)Note the update.config = TRUE parameter that will save the parameters
used in the call of att_amend_desc() to the package configuration
file: βdev/config_attachment.yamlβ.
If you run att_amend_desc() a second time afterwards, directly from
the console, it will use the last set of parameters extracted from the
configuration file.
Indeed, we recommend to store the complete command line in a
βdev/dev_history.Rβ file to update and run it when needed. If the
parameters do not change, you can run attachment::att_amend_desc()
directly in the console, wherever you are, it will use the configuration
file.
Automatically fill the βRemotesβ field
If you would like to detect the sources of your installations so that you can add dependencies in the βRemotesβ field of your DESCRIPTION file, to mimic your local installation, you will use:
attachment::set_remotes_to_desc()Example on a fake package
# Copy example package in a temporary directory
tmpdir <- tempfile(pattern = "fakepkg")
dir.create(tmpdir)
file.copy(system.file("dummypackage",package = "attachment"), tmpdir, recursive = TRUE)
#> [1] TRUE
dummypackage <- file.path(tmpdir, "dummypackage")
# browseURL(dummypackage)
# Fill the DESCRIPTION file automatically
# `inside_rmd` is specifically designed here to allow to run this command line in the "Readme.Rmd" file
desc_file <- attachment::att_amend_desc(path = dummypackage, inside_rmd = TRUE, update.config = TRUE)
#> 'update.config' was set to TRUE, hence, 'use.config' was forced to FALSE
#> Saving attachment parameters to yaml config file
#> Updating dummypackage documentation
#> ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
#> Changes in roxygen2 7.0.0:
#> * `%` is now escaped automatically in Markdown mode.
#> Please carefully check .Rd files for changes
#> ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
#>
#> Setting `RoxygenNote` to "7.2.2"
#> βΉ Loading dummypackage
#> Writing 'οΏ½]8;;file:///tmp/Rtmp3Dpn4h/fakepkg3538450e5c49/dummypackage/NAMESPACEοΏ½NAMESPACEοΏ½]8;;οΏ½'
#> Writing 'οΏ½]8;;file:///tmp/Rtmp3Dpn4h/fakepkg3538450e5c49/dummypackage/NAMESPACEοΏ½NAMESPACEοΏ½]8;;οΏ½'
#> βΉ Loading dummypackage
#> Package(s) Rcpp is(are) in category 'LinkingTo'. Check your Description file to be sure it is really what you want.
#>
#> [-] 1 package(s) removed: utils.
#>
#> [+] 2 package(s) added: stats, glue.
# Add Remotes if you have some installed
attachment::set_remotes_to_desc(path.d = desc_file)
#> There are no remote packages installed on your computer to add to description
#> NULL
# Clean state
unlink(tmpdir, recursive = TRUE)More on finding Remotes repositories (non installed from CRAN)
Find packages installed out of CRAN. This helps fill the βRemotesβ field
in DESCRIPTION file with set_remotes_to_desc().
Behind the scene, it uses find_remotes().
- See the examples below if {fusen} is installed from GitHub
- Also works for GitLab, Bioconductor, Git, Local installations
# From GitHub
remotes::install_github("ThinkR-open/fusen",
quiet = TRUE, upgrade = "never")
attachment::find_remotes("fusen")
#> $fusen
#> [1] "ThinkR-open/fusen"Find and install missing dependencies required for your R scripts
To quickly install missing packages from a DESCRIPTION file, use:
attachment::install_from_description()
#> All required packages are installedTo quickly install missing packages needed to compile Rmd files or run R scripts, use:
attachment::att_from_rmds(path = ".") |> attachment::install_if_missing()
attachment::att_from_rscripts(path = ".") |> attachment::install_if_missing()Function attachment::create_dependencies_file() will create a
dependencies.R file in inst/ directory. This R script contains the
procedure to quickly install missing dependencies:
# Remotes ----
# remotes::install_github("ThinkR-open/fcuk")
# Attachments ----
to_install <- c("covr", "desc", "devtools", "glue", "knitr", "magrittr", "rmarkdown", "stats", "stringr", "testthat", "utils")
for (i in to_install) {
message(paste("looking for ", i))
if (!requireNamespace(i)) {
message(paste(" installing", i))
install.packages(i)
}
}Allow the CI to install all dependencies required for your bookdown, pagedown, quarto, β¦
If you write a {bookdown} and want to publish it on Github using GitHub
Actions or GitLab CI for instance, you will need a DESCRIPTION file with
list of dependencies just like for a package. In this case, you can use
the function to description from import/suggest:
att_to_desc_from_is().
usethis::use_description()
# bookdown Imports are in Rmds
imports <- c("bookdown", attachment::att_from_rmds("."))
attachment::att_to_desc_from_is(path.d = "DESCRIPTION",
imports = imports, suggests = NULL)Then, install dependencies with
remotes::install_deps()List packages required in any script or notebook
Of course, you can also use {attachment} out of a package to list all
package dependencies of R scripts using att_from_rscripts() or Rmd/qmd
files using att_from_rmds().
If you are running this inside a Rmd, you may need parameter
inside_rmd = TRUE.
library(attachment)
dummypackage <- system.file("dummypackage", package = "attachment")
att_from_rscripts(path = dummypackage)
#> [1] "stats" "testthat" "dummypackage"
att_from_rmds(path = file.path(dummypackage, "vignettes"), inside_rmd = TRUE)
#> [1] "knitr" "rmarkdown" "glue"Vignettes included
Package {attachment} has vignettes to present the different functions
available. There is also a recommendation to have a dev_history.R in
the root directory of your package. (Have a look at
dev_history.R
in the present package)
vignette("a-fill-pkg-description", package = "attachment")
vignette("b-bookdown-and-scripts", package = "attachment")
vignette("use_renv", package = "attachment")
vignette("create-dependencies-file", package = "attachment")The vignettes are available on the {pkgdown} page, in the βArticlesβ menu: https://thinkr-open.github.io/attachment/
Code of Conduct
Please note that the attachment project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms