Efficient dependency management with {renv}

.title[
# Efficient dependency management with {renv}
]
.author[
### Julia Romanowska
]
.date[
### 2023-03-15
]

---

## {renv} package

---

## Why?

### reproducibility

???

One of the points to consider when creating reproducible code is the versions 
of software one uses.

### peace of mind

???

Remember the last time you needed to get back to a project after a longer break
and suddenly you get some errors because packages were updated in the meantime?

### collaboration

???

No need to ask collaborators to try to re-install certain packages after your 
code would not run on their machines!

---

## <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M112.1 454.3c0 6.297 1.816 12.44 5.284 17.69l17.14 25.69c5.25 7.875 17.17 14.28 26.64 14.28h61.67c9.438 0 21.36-6.401 26.61-14.28l17.08-25.68c2.938-4.438 5.348-12.37 5.348-17.7L272 415.1h-160L112.1 454.3zM191.4 .0132C89.44 .3257 16 82.97 16 175.1c0 44.38 16.44 84.84 43.56 115.8c16.53 18.84 42.34 58.23 52.22 91.45c.0313 .25 .0938 .5166 .125 .7823h160.2c.0313-.2656 .0938-.5166 .125-.7823c9.875-33.22 35.69-72.61 52.22-91.45C351.6 260.8 368 220.4 368 175.1C368 78.61 288.9-.2837 191.4 .0132zM192 96.01c-44.13 0-80 35.89-80 79.1C112 184.8 104.8 192 96 192S80 184.8 80 176c0-61.76 50.25-111.1 112-111.1c8.844 0 16 7.159 16 16S200.8 96.01 192 96.01z"/></svg> How?

1. `renv::init()`

1. work as usual

1. `renv::snapshot()`

1. work as usual

1. `renv::snapshot()` or `renv::restore()`

???

1. Call `renv::init()` to initialize a new project-local environment with a
private R library,

1. Work in the project as normal, installing and removing new R packages as
they are needed in the project,

1. Call `renv::snapshot()` to save the state of the project library to the
lockfile (called renv.lock),

1. Continue working on your project, installing and updating R packages as
needed.

1. Call `renv::snapshot()` again to save the state of your project library if your
attempts to update R packages were successful, or call `renv::restore()` to revert
to the previous state as encoded in the lockfile if your attempts to update
packages introduced some new problems.

> `snapshot()` records: pkg version and installation source

> `restore()` attempts to re-install the packages based on the info saved

---

## Details - file structure

- <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg> `.Rprofile`
- <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg> `renv.lock`
- <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg> `renv/activate.R`
- <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M512 144v288c0 26.5-21.5 48-48 48h-416C21.5 480 0 458.5 0 432v-352C0 53.5 21.5 32 48 32h160l64 64h192C490.5 96 512 117.5 512 144z"/></svg> `renv/library`
- <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg> `renv/settings.dcf`
]

.pull-right[
<br>
<br>
&larr; _commit to git_    
&larr; _commit to git_    
&larr; _commit to git_    
&larr; _ignore in git_
]

???

| File  |	Usage |
|-------|-------|
| .Rprofile |	Used to activate renv for new R sessions launched in the project. |
| renv.lock |	The lockfile, describing the state of your project’s library at some point in time. |
| renv/activate.R |	The activation script run by the project .Rprofile. |
| renv/library |	The private project library. |
| renv/settings.dcf |	Project settings – see ?settings for more details. |

---

## Details - dependency discovery

- `renv::dependencies()` searches for `library()` calls

???

This should work, but sometimes we're using only one function from a package,
without loading it. Or the package is not easily found in standard sources.
Or we don't want {renv} to search through some files. We can adjust that manually.

- you can create <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg> `_dependencies.R` with only `library()` calls

- use <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg> `.gitignore` and <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg>`.renvignore`

- add <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M0 64C0 28.65 28.65 0 64 0H224V128C224 145.7 238.3 160 256 160H384V448C384 483.3 355.3 512 320 512H64C28.65 512 0 483.3 0 448V64zM256 128V0L384 128H256z"/></svg> `DESCRIPTION` file to the project

???

- `_dependencies.R` or `DESCRIPTION` works in a similar way: telling {renv}
which packages to include _explicitly_

- `.renvignore` lists files that {renv} should not read

---

## Details - cache

- packages live in global _cache_ = _main library dir_

- <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M512 144v288c0 26.5-21.5 48-48 48h-416C21.5 480 0 458.5 0 432v-352C0 53.5 21.5 32 48 32h160l64 64h192C490.5 96 512 117.5 512 144z"/></svg> `library` in each project has links to cache

???

Use of cached packages makes `restore()` and `install()` faster and saves disk
space. You can always disable cache for each project separately or globally.

> _NOTE: this will not work across disks on Windows!_

???

If you're working on a network disk but have all the libraries installed on a
local disk, you should either move the projects to the local disk or the main
library to a network disk.

---

## <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M506.3 417l-213.3-364c-16.33-28-57.54-28-73.98 0l-213.2 364C-10.59 444.9 9.849 480 42.74 480h426.6C502.1 480 522.6 445 506.3 417zM232 168c0-13.25 10.75-24 24-24S280 154.8 280 168v128c0 13.25-10.75 24-23.1 24S232 309.3 232 296V168zM256 416c-17.36 0-31.44-14.08-31.44-31.44c0-17.36 14.07-31.44 31.44-31.44s31.44 14.08 31.44 31.44C287.4 401.9 273.4 416 256 416z"/></svg> Caveats

- takes care only of R-packages (see also `?renv::equip()`)

- package version needs to be available (online/offline) - _default sources_

- CRAN,
    - GitHub/Gitlab,
    - Bioconductor,
    - Bitbucket

- all things reproducibility:    
<svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:gray;overflow:visible;position:relative;"><path d="M448 336v-288C448 21.49 426.5 0 400 0H96C42.98 0 0 42.98 0 96v320c0 53.02 42.98 96 96 96h320c17.67 0 32-14.33 32-31.1c0-11.72-6.607-21.52-16-27.1v-81.36C441.8 362.8 448 350.2 448 336zM143.1 128h192C344.8 128 352 135.2 352 144C352 152.8 344.8 160 336 160H143.1C135.2 160 128 152.8 128 144C128 135.2 135.2 128 143.1 128zM143.1 192h192C344.8 192 352 199.2 352 208C352 216.8 344.8 224 336 224H143.1C135.2 224 128 216.8 128 208C128 199.2 135.2 192 143.1 192zM384 448H96c-17.67 0-32-14.33-32-32c0-17.67 14.33-32 32-32h288V448z"/></svg> [Building reproducible analytical pipelines with R](https://raps-with-r.dev/)

???

This is not a panaceum! If an R-package depends on an external library, this
will have to be installed manually. `renv::equip()` can help for some software
on Windows.

Copy of the version of the package needs to be either online or offline.

You can add sources manually, through settings - check
[vignette for details](https://rstudio.github.io/renv/articles/renv.html#custom-r-package-repositories).

---

## What next?

- combine with docker <svg aria-hidden="true" role="img" viewBox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M349.9 236.3h-66.1v-59.4h66.1v59.4zm0-204.3h-66.1v60.7h66.1V32zm78.2 144.8H362v59.4h66.1v-59.4zm-156.3-72.1h-66.1v60.1h66.1v-60.1zm78.1 0h-66.1v60.1h66.1v-60.1zm276.8 100c-14.4-9.7-47.6-13.2-73.1-8.4-3.3-24-16.7-44.9-41.1-63.7l-14-9.3-9.3 14c-18.4 27.8-23.4 73.6-3.7 103.8-8.7 4.7-25.8 11.1-48.4 10.7H2.4c-8.7 50.8 5.8 116.8 44 162.1 37.1 43.9 92.7 66.2 165.4 66.2 157.4 0 273.9-72.5 328.4-204.2 21.4 .4 67.6 .1 91.3-45.2 1.5-2.5 6.6-13.2 8.5-17.1l-13.3-8.9zm-511.1-27.9h-66v59.4h66.1v-59.4zm78.1 0h-66.1v59.4h66.1v-59.4zm78.1 0h-66.1v59.4h66.1v-59.4zm-78.1-72.1h-66.1v60.1h66.1v-60.1z"/></svg>

- combine with git/GitHub <svg aria-hidden="true" role="img" viewBox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3 .3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5 .3-6.2 2.3zm44.2-1.7c-2.9 .7-4.9 2.6-4.6 4.9 .3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3 .7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3 .3 2.9 2.3 3.9 1.6 1 3.6 .7 4.3-.7 .7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3 .7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3 .7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>

- combine with CI/GitHub actions <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M305.8 2.076C314.4 5.932 320 14.52 320 24V64H336C406.7 64 464 121.3 464 192V358.7C492.3 371 512 399.2 512 432C512 476.2 476.2 512 432 512C387.8 512 352 476.2 352 432C352 399.2 371.7 371 400 358.7V192C400 156.7 371.3 128 336 128H320V168C320 177.5 314.4 186.1 305.8 189.9C297.1 193.8 286.1 192.2 279.9 185.8L199.9 113.8C194.9 109.3 192 102.8 192 96C192 89.2 194.9 82.71 199.9 78.16L279.9 6.161C286.1-.1791 297.1-1.779 305.8 2.077V2.076zM432 456C445.3 456 456 445.3 456 432C456 418.7 445.3 408 432 408C418.7 408 408 418.7 408 432C408 445.3 418.7 456 432 456zM112 358.7C140.3 371 160 399.2 160 432C160 476.2 124.2 512 80 512C35.82 512 0 476.2 0 432C0 399.2 19.75 371 48 358.7V153.3C19.75 140.1 0 112.8 0 80C0 35.82 35.82 .0004 80 .0004C124.2 .0004 160 35.82 160 80C160 112.8 140.3 140.1 112 153.3V358.7zM80 56C66.75 56 56 66.75 56 80C56 93.25 66.75 104 80 104C93.25 104 104 93.25 104 80C104 66.75 93.25 56 80 56zM80 408C66.75 408 56 418.7 56 432C56 445.3 66.75 456 80 456C93.25 456 104 445.3 104 432C104 418.7 93.25 408 80 408z"/></svg>