dozens of cardboard boxes — Manage your packages before they manage you. Photo by CHUTTERSNAP on Unsplash.

Summary

Managing dependencies is required when building packages. This post reviews some common functions and strategies. It doesn’t discuss including packages in the description or namespaces.

Overview
What packages are installed and where?
Package Management
The pak Package
Five Package States - R Packages
The renv package
The devtools functions
System Files
Sources of Confusion
Conclusion
Acknowledgements
References
Disclaimer
Reproducibility

Overview

What packages are installed and where?

This command shows what packages you are using and where they are installed on your system.

devtools::loaded_packages()[1:5, ]

   package
1  ggplot2
2 blogdown
3 ggthemes
4 devtools
5  usethis
                                                                     path
1  /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggplot2
2 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/blogdown
3 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ggthemes
4 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/devtools
5  /Library/Frameworks/R.framework/Versions/4.1/Resources/library/usethis

Package Management

These are common introductory commands for R users:

from CRAN, install.packages(pkgs = "dplyr").
Development version from GitHub, devtools::install_github("tidyverse/dplyr")
attach library to search path with library("dplyr").
for paths, run devtools::loaded_packages()
see list of attached packages search().
detach is the opposite of library. detach(package:dplyr)
verify package detached search()
remove package remove.packages("dplyr").
see installed packages installed.packages()

The `pak` Package

As of September 2022, Posit will probably recommend pak as its package installation tool, especially, for installing packages directly from GitHub.

pak::pkg_install("tibble")
pak::pkg_install("tidyverse/tibble")
pak::pkg_deps_tree("tibble")
pak::pkg_deps_explain("tibble", "rlang")
pak::local_install("cli")

Five Package States - R Packages

When you create a package, you are working on its source code. An R package can be in one of five states:

source. Source is the thing that is on GitHub or the raw code that a developer is creating.
bundled. A package compressed into a single file. In R, a bundled package uses the extension .tar.gz.
binary. Like a package bundle, a binary is a single file. Binaries are either Mac (extension .tgs) or Windows (extension zip). CRAN makes binaries. A developer submits a bundle and CRAN convert it to a binary.
installed. An installed package is a binary package that was decompressed into a package library.
in-memory. The familiar library(package) command puts the package in memory and on the search path.

The `renv` package

The renv package is the successor to packrat and is available in Rstudio version RStudio 2022.07.2. When choosing to create a package, a checkbox will appear that allows for renv to be installed.

More information is available on the website. I’m used to just calling library(package) or package::function(). When using renv you have to install it first even though it’s already in your local library.

call renv::init() to begin.
install and remove packages.
call renv::snapshot(). It saves a file renv.lock in the root directory that contains an inventory of the packages used.

The lockfile contents look like the code below:

{
  "R": {
    "Version": "4.1.3",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cran.rstudio.com"
      }
    ]
  },
  "Packages": {
    "R6": {
      "Package": "R6",
      "Version": "2.5.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "470851b6d5d0ac559e9d01bb352b4021",
      "Requirements": []
    },
  }
}

The `devtools` functions

These are the tools from the devtools package that I use the most. Alot of them are available via the RStudio GUI.

devtools::build() - Build package
devtools::build_rmd() - Build a Rmarkdown files package
devtools::build_site() - Execute ‘pkgdown’ build_site in a package
devtools::build_vignettes() - Build package vignettes.
devtools::check() - Check a package
devtools::document() - Document a package
devtools::load_all() - Load packages
devtools::spell_check() - One I should run more!

System Files

In building a package, I often include an rmarkdown document. The recommendation is for the document to be included in the inst folder. For example, the document would be included in the inst\article\index.Rmd. When the package is installed, the inst portion is omitted, leaving article\index.Rmd. Writing a function within the development version requires that it be referred to as a system file. The concept is detailed in the stackoverflow post: How to include RMarkdown file in r package?.

system.file("article", "index.Rmd", package = "myPackage")

Sources of Confusion

In R, library means a collection of packages and packages means software tools. This convention is counter to other programming languages.

Conclusion

When a developer creates his or her own package, it will in turn rely on other packages. Those packages will often times be outside of the base R package. (Although, I’ve seen some amazing coding where the author limits use to just functions in the base package.) Where a package incorporates the use of another package, it is referred to as a dependency. These dependencies must be explicit and inventoried. They must even include the specific versions. renv can help with that process. Also, remember that as a developer, you are writing source code and it may behave differently when it is bundled and installed in a user’s local library. Happy coding!

Acknowledgements

This blog post was made possible thanks to:

R Packages

References

[1]

R Core Team, R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing, 2022 [Online]. Available: https://www.R-project.org/

[2]

Y. Xie, C. Dervieux, and A. Presmanes Hill, Blogdown: Create blogs and websites with r markdown. 2022 [Online]. Available: https://CRAN.R-project.org/package=blogdown

[3]

H. Wickham, J. Hester, W. Chang, and J. Bryan, Devtools: Tools to make developing r packages easier. 2022 [Online]. Available: https://CRAN.R-project.org/package=devtools

[4]

G. Csárdi and J. Hester, Pak: Another approach to package installation. 2022 [Online]. Available: https://pak.r-lib.org/

[5]

K. Ushey, Renv: Project environments. 2022 [Online]. Available: https://rstudio.github.io/renv/

Disclaimer

The views, analysis and conclusions presented within this paper represent the author’s alone and not of any other person, organization or government entity. While I have made every reasonable effort to ensure that the information in this article was correct, it will nonetheless contain errors, inaccuracies and inconsistencies. It is a working paper subject to revision without notice as additional information becomes available. Any liability is disclaimed as to any party for any loss, damage, or disruption caused by errors or omissions, whether such errors or omissions result from negligence, accident, or any other cause. The author(s) received no financial support for the research, authorship, and/or publication of this article.

Reproducibility

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.1.3 (2022-03-10)
 os       macOS Big Sur/Monterey 10.16
 system   x86_64, darwin17.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2022-12-08
 pandoc   2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version    date (UTC) lib source
 assertthat    0.2.1      2019-03-21 [1] CRAN (R 4.1.0)
 blogdown    * 1.13       2022-09-24 [1] CRAN (R 4.1.2)
 bookdown      0.29       2022-09-12 [1] CRAN (R 4.1.3)
 bslib         0.4.1.9900 2022-12-08 [1] Github (rstudio/bslib@1a07d5e)
 cachem        1.0.6      2021-08-19 [1] CRAN (R 4.1.0)
 callr         3.7.2      2022-08-22 [1] CRAN (R 4.1.2)
 cli           3.4.1      2022-09-23 [1] CRAN (R 4.1.2)
 codetools     0.2-18     2020-11-04 [1] CRAN (R 4.1.3)
 colorspace    2.0-3      2022-02-21 [1] CRAN (R 4.1.2)
 crayon        1.5.2      2022-09-29 [1] CRAN (R 4.1.3)
 DBI           1.1.3      2022-06-18 [1] CRAN (R 4.1.2)
 devtools    * 2.4.4      2022-07-20 [1] CRAN (R 4.1.2)
 digest        0.6.30     2022-10-18 [1] CRAN (R 4.1.2)
 dplyr         1.0.10     2022-09-01 [1] CRAN (R 4.1.2)
 ellipsis      0.3.2      2021-04-29 [1] CRAN (R 4.1.0)
 evaluate      0.18       2022-11-07 [1] CRAN (R 4.1.2)
 fansi         1.0.3      2022-03-24 [1] CRAN (R 4.1.2)
 fastmap       1.1.0      2021-01-25 [1] CRAN (R 4.1.0)
 formatR       1.12       2022-03-31 [1] CRAN (R 4.1.2)
 fs            1.5.2      2021-12-08 [1] CRAN (R 4.1.0)
 generics      0.1.3      2022-07-05 [1] CRAN (R 4.1.2)
 ggplot2     * 3.4.0      2022-11-04 [1] CRAN (R 4.1.2)
 ggthemes    * 4.2.4      2021-01-20 [1] CRAN (R 4.1.0)
 glue          1.6.2      2022-02-24 [1] CRAN (R 4.1.2)
 gtable        0.3.1      2022-09-01 [1] CRAN (R 4.1.2)
 htmltools     0.5.4.9000 2022-12-08 [1] Github (rstudio/htmltools@f53be17)
 htmlwidgets   1.5.4      2021-09-08 [1] CRAN (R 4.1.0)
 httpuv        1.6.6      2022-09-08 [1] CRAN (R 4.1.2)
 jquerylib     0.1.4      2021-04-26 [1] CRAN (R 4.1.0)
 jsonlite      1.8.4      2022-12-06 [1] CRAN (R 4.1.3)
 knitr         1.41       2022-11-18 [1] CRAN (R 4.1.2)
 later         1.3.0      2021-08-18 [1] CRAN (R 4.1.0)
 lifecycle     1.0.3      2022-10-07 [1] CRAN (R 4.1.2)
 magrittr      2.0.3      2022-03-30 [1] CRAN (R 4.1.2)
 memoise       2.0.1      2021-11-26 [1] CRAN (R 4.1.0)
 mime          0.12       2021-09-28 [1] CRAN (R 4.1.0)
 miniUI        0.1.1.1    2018-05-18 [1] CRAN (R 4.1.0)
 munsell       0.5.0      2018-06-12 [1] CRAN (R 4.1.0)
 pillar        1.8.1      2022-08-19 [1] CRAN (R 4.1.2)
 pkgbuild      1.3.1      2021-12-20 [1] CRAN (R 4.1.0)
 pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.1.0)
 pkgload       1.3.0      2022-06-27 [1] CRAN (R 4.1.2)
 prettyunits   1.1.1      2020-01-24 [1] CRAN (R 4.1.0)
 processx      3.8.0      2022-10-26 [1] CRAN (R 4.1.2)
 profvis       0.3.7      2020-11-02 [1] CRAN (R 4.1.0)
 promises      1.2.0.1    2021-02-11 [1] CRAN (R 4.1.0)
 ps            1.7.2      2022-10-26 [1] CRAN (R 4.1.2)
 purrr         0.3.5      2022-10-06 [1] CRAN (R 4.1.2)
 R6            2.5.1      2021-08-19 [1] CRAN (R 4.1.0)
 Rcpp          1.0.9      2022-07-08 [1] CRAN (R 4.1.2)
 remotes       2.4.2      2021-11-30 [1] CRAN (R 4.1.0)
 rlang         1.0.6      2022-09-24 [1] CRAN (R 4.1.2)
 rmarkdown     2.18       2022-11-09 [1] CRAN (R 4.1.3)
 rstudioapi    0.14       2022-08-22 [1] CRAN (R 4.1.2)
 sass          0.4.4      2022-11-24 [1] CRAN (R 4.1.2)
 scales        1.2.1      2022-08-20 [1] CRAN (R 4.1.2)
 sessioninfo   1.2.2      2021-12-06 [1] CRAN (R 4.1.0)
 shiny         1.7.2      2022-07-19 [1] CRAN (R 4.1.2)
 stringi       1.7.8      2022-07-11 [1] CRAN (R 4.1.2)
 stringr       1.5.0      2022-12-02 [1] CRAN (R 4.1.2)
 tibble        3.1.8.9002 2022-12-08 [1] Github (tidyverse/tibble@134e7ba)
 tidyselect    1.2.0      2022-10-10 [1] CRAN (R 4.1.2)
 urlchecker    1.0.1      2021-11-30 [1] CRAN (R 4.1.0)
 usethis     * 2.1.6      2022-05-25 [1] CRAN (R 4.1.2)
 utf8          1.2.2      2021-07-24 [1] CRAN (R 4.1.0)
 vctrs         0.5.1.9000 2022-12-08 [1] Github (r-lib/vctrs@48794fd)
 withr         2.5.0      2022-03-03 [1] CRAN (R 4.1.0)
 xfun          0.35       2022-11-16 [1] CRAN (R 4.1.2)
 xtable        1.8-4      2019-04-21 [1] CRAN (R 4.1.0)
 yaml          2.3.6      2022-10-18 [1] CRAN (R 4.1.2)

 [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Package Management in R

Summary

Table of Contents

Overview

What packages are installed and where?

Package Management

The `pak` Package

Five Package States - R Packages

The `renv` package

The `devtools` functions

System Files

Sources of Confusion

Conclusion

Acknowledgements

References

Disclaimer

Reproducibility

Package Management in R

Summary

Table of Contents

Overview

What packages are installed and where?

Package Management

The pak Package

Five Package States - R Packages

The renv package

The devtools functions

System Files

Sources of Confusion

Conclusion

Acknowledgements

References

Disclaimer

Reproducibility

The `pak` Package

The `renv` package

The `devtools` functions