Issues with renv 0.17.0 and 0.17.1

[zkamvar]

Note

We are leaving this issue open so that anyone who experiences issues know to upgrade {renv}

Recommendation

It is recommended for users to use {renv} version >= 0.17.2 (currently on CRAN) OR {renv} version <= 0.16.0.

Please run install.packages("renv") from your R console to upgrade.

---

Note

What follows below are protocols for when {renv} version 0.17.2 was not yet on CRAN.'
If you have {renv} version >= 0.17.2, then you do not need to do anything.

Test if you need to update your version of {renv}

To test if you need to update your version of {renv}, run this R code in your R console:

packageVersion("renv") > package_version("0.17.1")
#> [1] TRUE

If the result is TRUE, then you do not need to do anything.

If the result is FALSE, then follow one of the steps below.

Upgrading to the patched version: 0.17.0-38

To upgrade to the patched version of {renv}, use the following code to install renv version 0.17.0-38 from The Carpentries R-universe. Note: this is the version that {sandpaper} will use to build your R Markdown lessons on GitHub.

install.packages('renv', repos = c('https://carpentries.r-universe.dev', 'https://cloud.r-project.org'))

Note
renv 0.17.1 has a bug with its package cache (see rstudio/renv#1168) where the hashing changed.
This has been fixed in 0.17.2.

Downgrading to 0.16.0

If you wish to downgrade {renv} instead, you can install {renv} from an archive:

install.packages("https://cran.r-project.org/src/contrib/Archive/renv/renv_0.16.0.tar.gz")

Problem

The new version of {renv} 0.17.0 introduced a few unexpected bugs:

1. The renv/ folder now contains a locked sandbox folder, which causes teardown errors:

   rm: cannot remove '/tmp/Rtmp7JrJC1/Rbuild184d2b8b02c/sandpaper/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/99f2a2ef/spatial': Permission denied
   ... snip ...
   rm: cannot remove '/tmp/Rtmp7JrJC1/Rbuild184d2b8b02c/sandpaper/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/99f2a2ef/foreign': Permission denied
   

2. The welcome message has changed so our regex no longer works and causes R CMD check to fail:

   --- re-building ‘building-with-renv.Rmd’ using rmarkdown
   Quitting from lines 44-48 (building-with-renv.Rmd) 
   Error: Error: processing vignette 'building-with-renv.Rmd' failed with diagnostics:
   NA/NaN argument
   

3. BioConductor packages can no longer be provisioned or restored (see renv 0.17.0 issues with provisioning non-CRAN packages rstudio/renv#1156)
4. Continuous Integration is failing in ways that I cannot debug at the moment (see {renv} 0.17.0 cannot find rmarkdown on hydrate with bare project on CI rstudio/renv#1161 and [temporary fix] use devel renv #405)

Lessons Affected

• BioConductor Lessons can no longer restore their package cache
• New R Markdown lessons can no longer add new packages to the cache

All other existing lessons should work as expected.

[zkamvar]

Update

The issues presented have been fixed as of {renv} 0.17.0-38 🎉

Point 1 was fixed in rstudio/renv@8b5cb2c
Point 2 was easily addressed in c0f19a1 and 75506e3, which updated the message parsing.

Point 3 was not explicitly a BioConductor bug and was addressed in rstudio/renv@7aa92a0, which updated how r-universe repositories were handled.

Point 4 was fixed by rstudio/renv@028ccc5 and rstudio/renv@c068880, which updated the way R_LIBS_USER envvars were validated and how hydrate provisions source libraries.

Tasks left

• remove extra {renv} logging steps in [temporary fix] use devel renv #405
• fix revert hotfix for {renv} version 0.17.0 actions#70
• update universe to use correct version of {renv}
• ensure actions use correct version of {renv}

[zkamvar]

{renv} 0.17.1 has been released to CRAN. I will test this with the bioc lessons and then close this issue.

[zkamvar]

It does not break the bioc lessons, but #415 shows that there is something up with the reporting mechanism.

In addition, the hashing mechanism appears to be different

[zkamvar]

In addition, the hashing mechanism appears to be different

I see that someone else has noticed this: rstudio/renv#1168

[zkamvar]

What this means is that, because we make sure to rebuild if the package cache file has changed

sandpaper/inst/workflows/sandpaper-main.yaml

Line 59 in c8b911a

sandpaper::package_cache_trigger(TRUE)

then all R-based lessons will constantly go through a rebuild process until renv 0.17.2 is released.