GH actions failing after session this morning

[hulsiejames]

GH actions are failing after our coding session this morning @Robinlovelace on #56

Seems to be failing due to the following error within Run r-lib/actions/setup-r-dependencies@v1

  Error: Error: <callr_remote_error: Cannot install packages:
  * MASS: Needs R >= 4.3>
   in process 9022 
  -->
  <simpleError: Cannot install packages:
  * MASS: Needs R >= 4.3>

Full details on Run r-lib/actions/setup-r-dependencies@v1 below

Run r-lib/actions/setup-r-dependencies@v1
Run cat("::group::Install pak\n")
Install pak
Run cat("::set-output name=os-version::", sessionInfo()$running, "\n", sep = "")

Run actions/cache@v2
Received 121634816 of 248224025 (49.0%), 115.9 MBs/sec
Received 248224025 of 248224025 (100.0%), 117.7 MBs/sec
Cache Size: ~237 MB (248224025 B)
/usr/bin/tar --use-compress-program zstd -d -xf /home/runner/work/_temp/efc7ee09-1c0b-41b7-a1a6-06fabe7d74c2/cache.tzst -P -C /home/runner/work/openinfra/openinfra
Cache restored successfully

Cache restored from key: Ubuntu 20.04.4 LTS-R version 4.2.0 (2022-04-22)-1-3ee87c5ee5307601a2f33f13366ac29a59d84cffe7e8b1475daa459701f34202
Run cat("::group::Install dependencies\n")
Install dependencies
  ℹ Loading metadata database
  ✔ Loading metadata database ... done
  
  ℹ Executing `sudo apt-get install -y libcurl4-openssl-dev`
  ℹ Executing `sudo apt-get install -y libssl-dev`
  ℹ Executing `sudo apt-get install -y libudunits2-dev`
  ℹ Executing `sudo apt-get install -y libgdal-dev`
  ℹ Executing `sudo apt-get install -y gdal-bin`
  ℹ Executing `sudo apt-get install -y libgeos-dev`
  ℹ Executing `sudo apt-get install -y libproj-dev`
  ℹ Executing `sudo apt-get install -y zlib1g-dev`
  ℹ Executing `sudo apt-get install -y libicu-dev`
  ℹ Executing `sudo apt-get install -y make`
  ℹ Executing `sudo apt-get install -y libpng-dev`
  ℹ Executing `sudo apt-get install -y libxml2-dev`
  ℹ Executing `sudo apt-get install -y pandoc`
  ℹ Executing `sudo apt-get install -y libfontconfig1-dev`
  ℹ Executing `sudo apt-get install -y libfreetype6-dev`
  ℹ Executing `sudo apt-get install -y imagemagick`
  ℹ Executing `sudo apt-get install -y libmagick++-dev`
  ℹ Executing `sudo apt-get install -y gsfonts`
  ℹ Executing `sudo apt-get install -y libcurl4-openssl-dev`
  ℹ Executing `sudo apt-get install -y libssl-dev`
  
  Error: Error: <callr_remote_error: Cannot install packages:
  * MASS: Needs R >= 4.3>
   in process 9022 
  -->
  <simpleError: Cannot install packages:
  * MASS: Needs R >= 4.3>
  
   Stack trace:
  
   12. (function (...)  ...
   13. base:::withCallingHandlers(cli_message = function(msg) { ...
   14. get("pkg_install_make_plan", asNamespace("pak"))(...)
   15. prop$stop_for_solution_error()
   16. private$plan$stop_for_solve_error()
   17. pkgdepends:::pkgplan_stop_for_solve_error(self, private)
   18. base:::stop("Cannot install packages:\n", msg, call. = FALSE)
   19. base:::.handleSimpleError(function (e)  ...
   20. h(simpleError(msg, call))
   21. base:::stop(e)
   22. (function (e)  ...
  
   x Cannot install packages:
  * MASS: Needs R >= 4.3 
  
  Execution halted
  Error: Process completed with exit code 1.

[Robinlovelace]

Should be a self fixing bug. I bet other people are seeing this.

[hulsiejames]

Good to hear! Was worried I might have been using a different R version and that could be the issue.

Will re-try these later on and then tomorrow and update.

[hulsiejames]

Updates:
I've been trying to re-run all failed jobs a number of times the last couple of days however have had no luck.

I went to our pkgdown.yaml and R-CMD-check.yaml and followed the link for debugging build failures and have noticed that
/setup-r@v2,
/setup-r-dependencies@v2,
/setup-pandoc@v2
all have v2 versions available which are used in examples on the linked documentation pages, whilst we still use v1 for these. (We already use checkout@v2)

I also notice that within the setup-r@v2 basic example, a version of R can be specified

steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v2
  with:
    r-version: '3.5.3' # The R version to download (if necessary) and use.
- run: Rscript -e 'print("hello")'

@Robinlovelace I'm not too sure if this is even relevant/helpful to the issue, I didn't want to go editing these files/configs not fully understanding what I'd be changing!

[Robinlovelace]

Maybe try re-running usethis::use_github_actions() type functions and see what happens.

[hulsiejames]

Tried the follwoing after looking at the help documentation:

First I tried:

> use_github_action(name = "pkgdown.yaml")
✔ Saving 'r-lib/actions/examples/pkgdown.yaml@v1' to '.github/workflows/pkgdown.yaml'
• Learn more at <https://github.com/r-lib/actions/blob/v1/examples/README.md>.

but contrary to the documentation on use_github_action (below) it has used yaml@v1 rather than yaml@v2

---

name
For use_github_action(): Name of one of the example workflows from https://github.com/r-lib/actions/tree/v2/examples. Examples: "pkgdown", "check-standard.yaml"."

---

I then noticed that use_github_action also accepts a full url link to a valid .yaml file

---

url
The full URL to a .yaml file on GitHub.

---

As such, I re-tried using use_github_action specifying the full ulr to the raw pkgdown.yaml@v2 file

>  help("use_github_actions")

>  help("use_github_action")

>  use_github_action(name = "pkgdown.yaml", url="https://github.com/r-lib/actions/raw/v2-branch/examples/pkgdown.yaml")
Error: Can't parse the URL provided via `repo_spec`.

>  use_github_action(name = "pkgdown.yaml", repo_spec= "r-lib/actions", url="https://github.com/r-lib/actions/raw/v2-branch/examples/pkgdown.yaml")
Error in use_github_action(name = "pkgdown.yaml", repo_spec = "r-lib/actions",  : 
  unused argument (repo_spec = "r-lib/actions")

>  use_github_action(name = "pkgdown.yaml", repo_spec=r-lib/actions, url="https://github.com/r-lib/actions/raw/v2-branch/examples/pkgdown.yaml")
Error in use_github_action(name = "pkgdown.yaml", repo_spec = r - lib/actions,  : 
  unused argument (repo_spec = r - lib/actions)

>  use_github_action(name = "pkgdown.yaml", repo_spec=NULL, url="https://github.com/r-lib/actions/raw/v2-branch/examples/pkgdown.yaml")
Error in use_github_action(name = "pkgdown.yaml", repo_spec = NULL, url = "https://github.com/r-lib/actions/raw/v2-branch/examples/pkgdown.yaml") : 
  unused argument (repo_spec = NULL)

>  use_github_action(name = "pkgdown.yaml", url="https://github.com/r-lib/actions/raw/v2-branch/examples/pkgdown.yaml")
Error: Can't parse the URL provided via `repo_spec`.
>  use_github_action_check_release()
✔ Saving 'r-lib/actions/examples/check-release.yaml@v1' to '.github/workflows/R-CMD-check.yaml'
Overwrite pre-existing file '.github/workflows/R-CMD-check.yaml'?

1: No way
2: I agree
3: Absolutely not

> Selection: 2
• Learn more at <https://github.com/r-lib/actions/blob/v1/examples/README.md>.

However I kept getting errors about unused argument repo_spec which I could not understand or debug online.

Next I saw that use_github_action_check_releases seemed to install the latest version of R and ran the R-CMD-check, I ran this as can be seen in the code block above.

I created a backup of both of our existing workflow.yaml files incase anything went very wrong.

After running this the the R-CMD-check.yaml was modified and I pushed to the repo:

Again, the resulting workflows failed with the same error as before:

  Error: Error: <callr_remote_error: Cannot install packages:
  * MASS: Needs R >= 4.3>
   in process 8678 
  -->
  <simpleError: Cannot install packages:
  * MASS: Needs R >= 4.3>

Within the failed workflow run, under the Run r-lib/actions/setup-r@v1 section I noticed the following lines of interest.

809 - /usr/bin/sudo gdebi --non-interactive /home/runner/work/_temp/r-4.2.0_1_amd64.deb

*unimportant lines*

936 -  Selecting previously unselected package r-4.2.0.
937 -  (Reading database ... 247999 files and directories currently installed.)
938 -  Preparing to unpack .../work/_temp/r-4.2.0_1_amd64.deb ...
939 -  Unpacking r-4.2.0 (1) ...
940 -  Setting up r-4.2.0 (1) ...
941 - 
942 - 
943 - Reading state information... Done
944 - /usr/bin/sudo ln -sf /opt/R/4.2.0/bin/R /usr/local/bin/R
945 - /usr/bin/sudo ln -sf /opt/R/4.2.0/bin/Rscript /usr/local/bin/Rscript
946 - /usr/bin/lsb_release --short --codename
947 - focal

Suggesting that R 4.2 is being installed which explains the R >= 4.3 requirement for MASS that is failing the workflow.

I was going to try and specify an R>=4.3 using the approach (below) from my previous update, however searching for the latest version of R revealed that 4.2 is the most up-to-date 🤷‍♂️

steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v2
  with:
    r-version: '3.5.3' # The R version to download (if necessary) and use.

As this did not fix the issue, I reverted the R-CMD-check.yaml back to Robin's previous edit.

[Robinlovelace]

Was worth a try! Not urgent I can take a look at some point but won't be until in a few weeks time but which point their may be upstream fixes.

[hulsiejames]

very short and final update:

from the CRAN package page for MASS:

MASS: Support Functions and Datasets for Venables and Ripley's MASS
Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

Version: | 7.3-57
-- | --
Priority: | recommended
**Depends: | R (≥ 3.3.0), grDevices, graphics, stats, utils**

There must be a typo or something somewhere listing MASS depending on 4.3, when it is actually 3.3.
I assume could be fixed within the coming days/weeks.

[hulsiejames]

Issue has been fixed!

Seemed to be that using v1 rather than v2 was the cause.

Tto fix this I simply manually bumped up the versions of r-lib/actions by changing pkgdown.yaml and R-CMD-check.yaml within the .github/workflows/ directory.

This fixed the MASS R >=4.3 error, but created a few more listed below.

For anyone else with this issue:

1. I manually updated my pkgdown & R-CMD-check .yaml file uses prefixes from "v1" to "v2"
2. This created the following error:

  Error: Error: <callr_remote_error: Cannot install packages:
  * pkgdown: dependencies must be TRUE, FALSE, NA or a list of dependency types>
   in process 8881 

3. The error is fixable changing extra-packages:pkgdown to any::pkgdown. Shown here
4. A new error was created after applying the above fix. Now:

  Error: Error: <callr_remote_error: Failed to build source package 'XML'>
   in process 8256 
  -->
  Failed to build source package 'XML', stdout + stderr:

5. This is a known pak error, and like above is fixable by adding any::XML to the extra-packages field in your .yaml

Closing now as this seems to be fixed. Hope this helps if you have a similar issue.