settings.json file with empty r.version causes failure

[zkamvar]

Once again, I am finding myself caught in a situation where something has changed and I do not know what it is. Here is a reprex (that uses the packages for {knitr}), but I will work on producing a minimal one:

remotes::install_github("rstudio/renv@43ab2f25bef0c53e544126723312618fb547929a")
install.packages(c("sandpaper", "varnish"), repos = c("https://carpentries.r-universe.dev", "https://cran.rstudio.com"))

usethis::create_from_github("carpentries/sandpaper-docs")
sandpaper::build_lesson()

reprex output

> usethis::create_from_github("carpentries/sandpaper-docs")                                                                                                                   
✔ Setting `fork = FALSE`
✔ Creating '/home/zhian/Desktop/sandpaper-docs/'
✔ Cloning repo from 'https://github.com/carpentries/sandpaper-docs.git' into '/home/zhian/Desktop/sandpaper-docs'
✔ Setting active project to '/home/zhian/Desktop/sandpaper-docs'
ℹ Default branch is 'main'

> sandpaper::build_lesson()                                                                                                                                                   
── Validating Fenced Divs ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── Validating Internal Links and Images ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
! There were errors in 1/149 links
◌ Some linked internal files do not exist

episodes/episodes.Rmd:767 [missing file]: [Example of Wrapped Alt Text (with apologies to William Carlos Williams)](fig/freezer.png)
ℹ Consent to use package cache provided
→ Searching for and installing available dependencies
Done!ng R package dependencies ... 
Done!covering package dependencies ... 
The following packages were discovered:

# ~/R/library ========================
- base64enc     0.1-3
- bslib         0.4.2
- cachem        1.0.8
- cli           3.6.1
- digest        0.6.31
- ellipsis      0.3.2
- evaluate      0.21
- fastmap       1.1.1
- fontawesome   0.5.1
- fs            1.6.2
- glue          1.6.2
- highr         0.10
- htmltools     0.5.5
- jquerylib     0.1.4
- jsonlite      1.8.4
- knitr         1.42
- lifecycle     1.0.3
- magrittr      2.0.3
- memoise       2.0.1
- mime          0.12
- R6            2.5.1
- rappdirs      0.3.3
- rlang         1.1.1
- rmarkdown     2.21
- sass          0.4.6
- stringi       1.7.12
- stringr       1.5.0
- tinytex       0.45
- vctrs         0.6.2
- xfun          0.39
- yaml          2.3.7

They will be linked into the project library.

Done!king packages into the project library ... 
* Hydrated 31 packages in 71 milliseconds.
→ Restoring any dependency versions
The following package(s) will be updated:

# CRAN ===============================
- renv       [* -> 0.17.3]

# RSPM ===============================
- evaluate   [repo: CRAN -> RSPM; ver: 0.21 -> 0.20]
- sass       [repo: CRAN -> RSPM; ver: 0.4.6 -> 0.4.5]

Installing sass [0.4.5] ...
|       OK [linked cache in 0.28 milliseconds]
Installing evaluate [0.20] ...
-       OK [linked cache in 0.27 milliseconds]
Installing renv [0.17.3] ...
|       OK [linked cache in 0.31 milliseconds]
The following package(s) have been updated:

	renv [installed version 0.17.3 != loaded version 0.17.3-72]

Consider restarting the R session and loading the newly-installed packages.

→ Recording changes in lockfile
The version of R recorded in the lockfile will be updated:

* Lockfile written to '~/Desktop/sandpaper-docs/renv/profiles/lesson-requirements/renv.lock'.
ℹ Using package cache in /home/zhian/.cache/R/renv
Error: 
! in callr subprocess.
Caused by error in `unclass(numeric_version(version))[[1]]`:
! subscript out of bounds
Type .Last.error to see the more details.

Session Information

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.0 (2023-04-21)
 os       Ubuntu 20.04.6 LTS
 system   x86_64, linux-gnu
 ui       X11
 language en_US:en
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Los_Angeles
 date     2023-05-26
 pandoc   2.12 @ /home/zhian/anaconda3/bin/ (via rmarkdown)

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version   date (UTC) lib source
 askpass       1.1       2019-01-13 [1] CRAN (R 4.0.0)
 assertthat    0.2.1     2019-03-21 [1] CRAN (R 4.0.0)
 callr         3.7.3     2022-11-02 [1] RSPM (R 4.2.0)
 cli           3.6.1     2023-03-23 [1] RSPM (R 4.2.0)
 commonmark    1.9.0     2023-03-17 [1] RSPM (R 4.2.0)
 credentials   1.3.2     2021-11-29 [1] CRAN (R 4.1.2)
 digest        0.6.31    2022-12-11 [1] RSPM (R 4.2.0)
 dplyr         1.1.2     2023-04-20 [1] RSPM (R 4.3.0)
 evaluate      0.21      2023-05-05 [1] RSPM (R 4.3.0)
 fansi         1.0.4     2023-01-22 [1] RSPM (R 4.2.0)
 fastmap       1.1.1     2023-02-24 [1] RSPM (R 4.2.0)
 fs            1.6.2     2023-04-25 [1] RSPM (R 4.3.0)
 generics      0.1.3     2022-07-05 [1] RSPM (R 4.2.0)
 gert          1.9.2     2022-12-05 [1] RSPM (R 4.2.0)
 glue          1.6.2     2022-02-24 [1] RSPM (R 4.2.0)
 htmltools     0.5.5     2023-03-23 [1] RSPM (R 4.2.0)
 knitr         1.42      2023-01-25 [1] CRAN (R 4.2.2)
 lifecycle     1.0.3     2022-10-07 [1] CRAN (R 4.2.1)
 magrittr      2.0.3     2022-03-30 [1] CRAN (R 4.1.3)
 openssl       2.0.6     2023-03-09 [1] RSPM (R 4.2.0)
 pegboard      0.5.3     2023-05-19 [1] Github (carpentries/pegboard@3b06f45)
 pillar        1.9.0     2023-03-22 [1] RSPM (R 4.2.0)
 pkgconfig     2.0.3     2019-09-22 [1] CRAN (R 4.0.4)
 processx      3.8.1     2023-04-18 [1] RSPM (R 4.3.0)
 ps            1.7.5     2023-04-18 [1] RSPM (R 4.3.0)
 purrr         1.0.1     2023-01-10 [1] RSPM (R 4.2.0)
 R6            2.5.1     2021-08-19 [1] CRAN (R 4.1.1)
 Rcpp          1.0.10    2023-01-22 [1] RSPM (R 4.2.0)
 renv          0.17.3-72 2023-05-26 [1] Github (rstudio/renv@43ab2f2)
 rlang         1.1.1     2023-04-28 [1] RSPM (R 4.3.0)
 rmarkdown     2.21      2023-03-26 [1] RSPM (R 4.2.0)
 rprojroot     2.0.3     2022-04-02 [1] CRAN (R 4.1.3)
 sandpaper   * 0.12.0    2023-05-24 [1] https://carpentries.r-universe.dev (R 4.3.0)
 sessioninfo   1.2.2     2021-12-06 [1] CRAN (R 4.1.2)
 sys           3.4.2     2023-05-23 [1] CRAN (R 4.3.0)
 tibble        3.2.1     2023-03-20 [1] RSPM (R 4.2.0)
 tidyselect    1.2.0     2022-10-10 [1] RSPM (R 4.2.0)
 tinkr         0.2.0     2023-05-19 [1] Github (ropensci/tinkr@a5dd3dd)
 utf8          1.2.3     2023-01-31 [1] RSPM (R 4.2.0)
 vctrs         0.6.2     2023-04-19 [1] RSPM (R 4.3.0)
 whisker       0.4.1     2022-12-05 [1] RSPM (R 4.2.0)
 xfun          0.39      2023-04-20 [1] RSPM (R 4.3.0)
 xml2          1.3.4     2023-04-27 [1] RSPM (R 4.3.0)
 xslt          1.4.4     2023-02-21 [1] RSPM (R 4.2.0)
 yaml          2.3.7     2023-01-23 [1] RSPM (R 4.2.0)

 [1] /home/zhian/R/library
 [2] /usr/local/lib/R/site-library
 [3] /usr/lib/R/site-library
 [4] /usr/lib/R/library

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

And here is the trackeback of the error, but this points to the fact that {renv} is trying to load a project that has no R version attached.

<callr_error/rlib_error_3_0/rlib_error/error>
Error: 
! in callr subprocess.
Caused by error in `unclass(numeric_version(version))[[1]]`:
! subscript out of bounds
---
Backtrace:
1. sandpaper::build_lesson()
2. sandpaper:::build_markdown(path = path, rebuild = rebuild, quiet = quiet, …
3. sandpaper::build_episode_md(path = build_me[i], outdir = outdir, workdir = outdir, …
4. callr::r(func = callr_build_episode_md, args = args, show = !quiet, …
5. callr:::get_result(output = out, options)
6. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
---
Subprocess backtrace:
1. renv::load(root)
2. renv:::renv_load_r(project, lockfile$R)
3. global (function (e) …

The diff for the lockfile looks like this:

 {
   "R": {
-    "Version": "4.3.0",
+    "Version": [],
     "Repositories": [
       {
         "Name": "carpentries",
@@ -256,6 +256,12 @@
       "Version": "0.12",
       "Source": "Repository",
       "Repository": "RSPM",
+      "RemoteType": "standard",
+      "RemotePkgRef": "mime",
+      "RemoteRef": "mime",
+      "RemoteRepos": "https://cran.rstudio.com",
+      "RemotePkgPlatform": "source",
+      "RemoteSha": "0.12",
       "Requirements": [
         "tools"
       ],
@@ -335,17 +341,13 @@
       "Version": "1.7.12",
       "Source": "Repository",
       "Repository": "RSPM",
-      "RemoteType": "repository",
-      "RemoteUrl": "https://github.com/gagolews/stringi",
-      "RemoteRef": "v1.7.12",
-      "RemoteSha": "e4cf3176bc3943e6c477885be3445cbbd7d4bab6",
       "Requirements": [
         "R",
         "stats",
         "tools",
         "utils"
       ],
-      "Hash": "832ef2a01603f8f5b4f2af024080d5d9"
+      "Hash": "ca8bd84263c77310739d2cf64d84d7c9"
     },
     "stringr": {
       "Package": "stringr",

[kevinushey]

My guess is the project contains an renv/settings.json file which contains:

"r.version": []

Are you explicitly calling renv::settings$r.version() anywhere, or doing anything else to try and set a default R version?

[zkamvar]

Are you explicitly calling renv::settings$r.version() anywhere, or doing anything else to try and set a default R version?

Not at all. We use a hydrate -> restore -> snapshot workflow

You are correct that the project contains a renv/profiles/lesson-requirements/renv/settings.json with an empty R version, which was added in carpentries/sandpaper-docs@b9ec78a.

I believe it's a holdover from when I first created the {renv} project back in January 2022, which created the settings.dcf file.

I've taken a look at some of the more recent repositories. They do not have the settings (i.e. datacarpentry/r-socialsci), and yet they work with this version of {renv} so I believe this will be fixed if I remove the settings files.

[kevinushey]

Thanks! I also pushed a bandaid to renv here: 6014f8d