pkgdown github action build error 'subscript out of bounds'

[jpiaskowski]

Hello,

I am having trouble getting a github action to complete a pkgdown site build. Here is my yaml file. I'm using the default template from rlibs for a pkgdown github action. The error is occurring within the step "r-lib/actions/setup-r-dependencies@v2", but where within that script is unclear to me. Here's a log file from the failed build (first error occurs at line 2676):

Error: Error: <callr_remote_error: subscript out of bounds>

The error may be occuring in this step in the 'setup-r-dependencies' file:

- name: Installing pak querying dependencies

(lines 69-91). However, I'm not sure about this and do not know how to proceed. This is clearly an R error indicating that an object is being indexed past its dimensions, but what this object is, how it was generated, etc, are not clear to me. I can build the pkgdown site locally with no problem. Package vignettes also build fine with pkgdown::build_articles(). Any suggestions? (Even for troublehshooting).

[jpiaskowski]

This appears to be a bug, so I will attempt the suggested workaround from that post.

[Gabor]

You'll need to show us the workflow file and the run that fails. Without these it is very hard to help you

[jpiaskowski]

I posted all the links to those (workflow, log, etc) in my original post...? They are long files, especially the log files, which is why I posted only the relevant error and where to find it in the log file. I am also this person. I was going to dig more into the file for 'setup-r-dependencies@v2' and see if I can identify where things go wrong.

[Gabor]

Right, sorry, I missed that. Unfortunately this seems to be a pak bug that comes out in certain cases for ?ignore.

If I add the repo to options(repos), then it works fine:

pak::repo_add(glmmADMB = "http://glmmadmb.r-forge.r-project.org/repos")
pak::lockfile_create(c("deps::.", "any::pkgdown", "local::."), dependencies = TRUE)
pak::lockfile_install()

This is how you can modify .Rprofile to add the other repo: actions/setup-r at v2 · r-lib/actions · GitHub Or maybe it is easier to use the extra-repositories parameter to add your extra repo.

[jpiaskowski]

I'm sorry, but I'm unclear about what to add and where. I added the repo as such between "setup-r@v2" and "setup-r-dependencies@v2":

      - name: set some special options for glmmADMB
        run: |
          cat('\noptions(repos = c("http://glmmadmb.r-forge.r-project.org/repos", 
          "https://cloud.r-project.org/"))', file = "~/.Rprofile", append = TRUE)
        shell: Rscript {0}

I can run the scripts you suggest (pak::repo_add(....)) in an interactive R session, but I don't understand where they belong in the workflow. When they are included in the .Rprofile, they fail.

[Gabor]

@jpiaskowski

I don't understand where they belong in the workflow.

That does not belong in the workflow, that was a test that I ran interactively.

Maybe it is easier to use the extra-repositories parameter instead of updating the R profile?

[jpiaskowski]

@Gabor

That does not belong in the workflow, that was a test that I ran interactively.

Yes, I gathered. That tests also works fine for me in an interactive, but the workflow still fails.

I don't know what process the "extra-packages" parameter refers to. I have spent hours looking at the documentation for pak, github actions and rlibs/actions, and this is just not clear. I'm going to stop working on this for the time being; it is just not worth anymore than the 20+ hours I've invested. Thank your for your time spent trying to help me resolve this. I kindly request you also do not spend any of your limited time trying to resolve my issue. Thank you again.