Get started
Authors: Brian Schilder
Authors: Brian Schilder
Vignette updated: Mar-16-2026
Source: Vignette updated: Mar-16-2026
vignettes/devoptera.Rmd
devoptera.RmdDevelopment workflow
Here, we show how devoptera can be used to greatly
accelerate your R package development workflow.
source_all
Let’s say you have many functions in your R folder and want
to have access to them all without having to write out the
pkg:::internal_func notation. You can source all the
functions at once by running devoptera::source_all.
This function can also load any R packages you need by supplying the
package names to the packages argument.
devoptera::source_all(packages = c("rlang","data.table"))## Loading required package: rlang## Loading required package: data.table##
## Attaching package: 'data.table'## The following object is masked from 'package:rlang':
##
## :=## The following object is masked from 'package:base':
##
## %notin%## Sourcing 19 files.
args2vars
As a developer, how often do you find yourself realizing there’s a bug somewhere inside your function? You could:
- Strategy 1: Edit –> Rebuild –> Repeat: Make a change to the code, rebuild the package, and rerun the function as a whole. This most closely mimics how it will run in production, but is extremely slow when iterating this edit-rebuild process many, many times over.
- Strategy 2: Run internal code line-by-line: Alternatively, you could go within your function, run one line of code at a time and inspect the variables it produces at each step. This is much faster than guessing whether your changes fixed the bug and rebuilding each time to find out whether they worked. But in order to do this, you first need to initialise each argument in your function as a global variable so that you can run the code line-by-line. But your function has many arguments, so now you spend the next minute(s) tediously making each argument into a variable of the same name (using the defaults as the assigned values).
devoptera::args2vars automates Strategy
2 by first running source_all (from previous
example) and then automatically assigning each of your function’s
arguments as global variables in your R environment. No more tedious
argument defining, allowing you to rapidly debug your code before going
to rebuild the entire package.
Define a function
Here we define an arbitrary function with 3 arguments. If your function is already in one of your source files (i.e. a .R file within the R/ subfolder), you can skip this step.
Convert arguments to variables
Now we will convert all the default arguments of myfunc
to global variables. It also returns a named list with each variable’s
assigned value.
args <- devoptera::args2vars(myfunc)## Sourcing 19 files.## Using input function.## Assigning '...' to 'NULL'## Assigning arguments of function: myfunc## Assigning global ->> a## Assigning global ->> b## Reassigning global ->> c
args## $a
## [1] 1
##
## $b
## [1] 2
##
## $c
## [1] 3After debugging your code, you can now proceed to the next steps.
Clear
Remove all variables using devoptera::rma(), or by
clicking the little broom in the upper right of your
Environment panel in RStudio.
This is important as it will ensure that the names of
functions/variables in your global environment (created with
source_all/args2vars) don’t override the
functions/variables within your reinstalled package (in the next
step).
devoptera::rma()Reinstall
(Re)install your package with devtools::install(), or by
clicking the Install button within the Build
panel in RStudio.
This is equivalent to the keystrokes
CMD+SHIFT+B within RStudio.
devtools::install()Check
Now you can recheck your package as usual to make sure everything runs as expected.
CRAN checks
The check function from devtools
runs R CMD check on your package.
This is equivalent to the keystrokes
CMD+SHIFT+E within RStudio.
devtools::check()Bioconductor checks
The BiocCheck function from BiocCheck
runs additional Bioconductor-specific checks.
BiocCheck::BiocCheck()If you still run into some bugs or unexpected behaviour, don’t worry! You can still easily go back and repeat this process until everything is working smoothly.
Extra functions
Restarting R
Restarting your R session can be helpful or necessary in a variety of situations. Not only does it clear your variables, it unloads all packages which is necessary when you want to use a package you just installed a new version of.
This is equivalent to the keystrokes
CMD+SHIFT+0 within RStudio.
devoptera::restart()Session Info
It is best practice to always include your R Session Info in any Rmarkdown report or vignette. It contains information about which OS, R version, and R package versions you generated the report with.
devoptera::session_info provides a collapsible version
of the Session Info, which can be helpful when Session Info is
particularly long.
devoptera::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R Under development (unstable) (2026-03-12 r89607)
## os Ubuntu 24.04.4 LTS
## system x86_64, linux-gnu
## ui X11
## language en
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz UTC
## date 2026-03-16
## pandoc 3.9 @ /usr/bin/ (via rmarkdown)
## quarto 1.8.27 @ /usr/local/bin/quarto
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## Biobase 2.71.0 2025-10-30 [1] Bioconductor 3.23 (R 4.6.0)
## BiocBaseUtils 1.13.0 2025-10-30 [1] Bioconductor 3.23 (R 4.6.0)
## BiocCheck 1.47.18 2026-02-03 [1] Bioconductor 3.23 (R 4.6.0)
## BiocFileCache 3.1.0 2025-10-30 [1] Bioconductor 3.23 (R 4.6.0)
## BiocGenerics 0.57.0 2025-10-30 [1] Bioconductor 3.23 (R 4.6.0)
## BiocManager 1.30.27 2025-11-14 [1] CRAN (R 4.6.0)
## BiocStyle * 2.39.0 2025-10-30 [1] Bioconductor 3.23 (R 4.6.0)
## biocViews 1.79.3 2026-02-25 [1] Bioconductor 3.23 (R 4.6.0)
## bit 4.6.0 2025-03-06 [1] CRAN (R 4.6.0)
## bit64 4.6.0-1 2025-01-16 [1] CRAN (R 4.6.0)
## bitops 1.0-9 2024-10-03 [1] CRAN (R 4.6.0)
## blob 1.3.0 2026-01-14 [1] CRAN (R 4.6.0)
## bookdown 0.46 2025-12-05 [1] CRAN (R 4.6.0)
## bslib 0.10.0 2026-01-26 [2] CRAN (R 4.6.0)
## cachem 1.1.0 2024-05-16 [2] CRAN (R 4.6.0)
## cli 3.6.5 2025-04-23 [2] CRAN (R 4.6.0)
## codetools 0.2-20 2024-03-31 [3] CRAN (R 4.6.0)
## curl 7.0.0 2025-08-19 [2] CRAN (R 4.6.0)
## data.table * 1.18.2.1 2026-01-27 [1] CRAN (R 4.6.0)
## DBI 1.3.0 2026-02-25 [1] CRAN (R 4.6.0)
## dbplyr 2.5.2 2026-02-13 [1] CRAN (R 4.6.0)
## desc 1.4.3 2023-12-10 [2] CRAN (R 4.6.0)
## devoptera * 1.0.0 2026-03-16 [1] Bioconductor
## devtools 2.4.6 2025-10-03 [2] CRAN (R 4.6.0)
## digest 0.6.39 2025-11-19 [2] CRAN (R 4.6.0)
## dplyr 1.2.0 2026-02-03 [1] CRAN (R 4.6.0)
## ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.6.0)
## evaluate 1.0.5 2025-08-27 [2] CRAN (R 4.6.0)
## fastmap 1.2.0 2024-05-15 [2] CRAN (R 4.6.0)
## filelock 1.0.3 2023-12-11 [1] CRAN (R 4.6.0)
## fs 1.6.7 2026-03-06 [2] CRAN (R 4.6.0)
## generics 0.1.4 2025-05-09 [1] CRAN (R 4.6.0)
## glue 1.8.0 2024-09-30 [2] CRAN (R 4.6.0)
## graph 1.89.1 2025-12-02 [1] Bioconductor 3.23 (R 4.6.0)
## here 1.0.2 2025-09-15 [1] CRAN (R 4.6.0)
## htmltools 0.5.9 2025-12-04 [2] CRAN (R 4.6.0)
## htmlwidgets 1.6.4 2023-12-06 [2] CRAN (R 4.6.0)
## httr2 1.2.2 2025-12-08 [2] CRAN (R 4.6.0)
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.6.0)
## jsonlite 2.0.0 2025-03-27 [2] CRAN (R 4.6.0)
## knitr 1.51 2025-12-20 [2] CRAN (R 4.6.0)
## lifecycle 1.0.5 2026-01-08 [2] CRAN (R 4.6.0)
## magrittr 2.0.4 2025-09-12 [2] CRAN (R 4.6.0)
## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.6.0)
## otel 0.2.0 2025-08-29 [2] CRAN (R 4.6.0)
## pillar 1.11.1 2025-09-17 [2] CRAN (R 4.6.0)
## pkgbuild 1.4.8 2025-05-26 [2] CRAN (R 4.6.0)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.6.0)
## pkgdown 2.2.0 2025-11-06 [1] CRAN (R 4.6.0)
## pkgload 1.5.0 2026-02-03 [2] CRAN (R 4.6.0)
## purrr 1.2.1 2026-01-09 [2] CRAN (R 4.6.0)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.6.0)
## R.oo 1.27.1 2025-05-02 [1] CRAN (R 4.6.0)
## R.utils 2.13.0 2025-02-24 [1] CRAN (R 4.6.0)
## R6 2.6.1 2025-02-15 [2] CRAN (R 4.6.0)
## ragg 1.5.1 2026-03-06 [2] CRAN (R 4.6.0)
## rappdirs 0.3.4 2026-01-17 [2] CRAN (R 4.6.0)
## RBGL 1.87.0 2025-10-30 [1] Bioconductor 3.23 (R 4.6.0)
## RCurl 1.98-1.17 2025-03-22 [1] CRAN (R 4.6.0)
## remotes 2.5.0.9000 2026-03-13 [1] Github (r-lib/remotes@6c988cc)
## rlang * 1.1.7 2026-01-09 [2] CRAN (R 4.6.0)
## rmarkdown 2.30 2025-09-28 [1] CRAN (R 4.6.0)
## rprojroot 2.1.1 2025-08-26 [2] CRAN (R 4.6.0)
## RSQLite 2.4.6 2026-02-06 [1] CRAN (R 4.6.0)
## rstudioapi 0.18.0 2026-01-16 [2] CRAN (R 4.6.0)
## RUnit 0.4.33.1 2025-06-17 [1] CRAN (R 4.6.0)
## sass 0.4.10 2025-04-11 [2] CRAN (R 4.6.0)
## sessioninfo 1.2.3 2025-02-05 [2] CRAN (R 4.6.0)
## stringdist 0.9.17 2026-01-16 [1] CRAN (R 4.6.0)
## systemfonts 1.3.2 2026-03-05 [2] CRAN (R 4.6.0)
## textshaping 1.0.5 2026-03-06 [2] CRAN (R 4.6.0)
## tibble 3.3.1 2026-01-11 [2] CRAN (R 4.6.0)
## tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.6.0)
## usethis 3.2.1 2025-09-06 [2] CRAN (R 4.6.0)
## vctrs 0.7.1 2026-01-23 [2] CRAN (R 4.6.0)
## xfun 0.56 2026-01-18 [2] CRAN (R 4.6.0)
## XML 3.99-0.22 2026-02-10 [1] CRAN (R 4.6.0)
## yaml 2.3.12 2025-12-10 [2] CRAN (R 4.6.0)
##
## [1] /__w/_temp/Library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
## * ── Packages attached to the search path.
##
## ──────────────────────────────────────────────────────────────────────────────