`?ignore`d packages is not ignored

[billdenney]

Related to #421, I'm trying to ignore the package lixoftConnectors when installing dependencies.

When I used lixoftConnectors?ignore in the extra-packages list, I got the following error indicating that it was not ignored:

https://github.com/nlmixr2/babelmixr2/actions/runs/3169455077/jobs/5161378366#step:5:109

The instructions I used were:

https://github.com/nlmixr2/babelmixr2/blob/5bd330353cf4ad0b62d0223b656246672119e3b1/.github/workflows/R-CMD-check.yaml#L45-L55

I was trying to follow the instructions here: https://github.com/r-lib/actions/tree/v2-branch/setup-r-dependencies#ignoring-optional-dependencies

[gaborcsardi]

The syntax is slightly different:

❯ pak::lockfile_create(c("deps::.", "lixoftConnectors=?ignore"), dependencies = TRUE)
✔ Created lockfile pkg.lock [547ms]

[billdenney]

First, thank you for being so responsive right now. It's very helpful to working through this issue (or these issues)!

I fixed the ignore syntax, but it appears to want to be able to find the package. I now see the same subscript out of bounds error as in #421.

I'm now trying adding the repository back in with extra-repositories: 'https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/'. (But my baby is waking up, so I'm now done working on it for several hours at least 😄 .)

[billdenney]

The installation is still not succeeding. I think that I've covered all the main steps as I see them documented:

• I am trying to ignore lixoftConnectors, the package that I don't need installed, (https://github.com/nlmixr2/babelmixr2/blob/930968565d70a20e7f4c715baf86e9ed2ded7dd3/.github/workflows/R-CMD-check.yaml#L56)
• And while I don't think it should be required, I added the repository that contains lixoftConnectors to the GitHub Action yaml file (https://github.com/nlmixr2/babelmixr2/blob/930968565d70a20e7f4c715baf86e9ed2ded7dd3/.github/workflows/R-CMD-check.yaml#L41)

Can you please help identify what the remaining issue is?

[gaborcsardi]

Can you link to the failing build?

[billdenney]

Here is the GitHub action log: https://github.com/nlmixr2/babelmixr2/actions/runs/3169571113

And, here is the commit that ran it: https://github.com/nlmixr2/babelmixr2/tree/930968565d70a20e7f4c715baf86e9ed2ded7dd3

If you were looking for something else, please let me know.

[gaborcsardi]

This was a bug in pkgdepends, unfortunately. I'll build new pak binaries and then GHA should be fine.

[gaborcsardi]

Try it again please, hopefully it works now.

[billdenney]

@gaborcsardi , I ran this again about 2 hours ago (without modification), and I was still getting the same issue. Should it have succeeded or is there a delay for changes to propogate?

https://github.com/nlmixr2/babelmixr2/actions/runs/3169571113/jobs/5172821660 (note that the running time is 1 hour ago)

[gaborcsardi]

It was deployed less than an hour ago.

[billdenney]

Success! Thank you!

(Well, I still have some work to do as there are testing errors, but the CI seems to be working correctly. 😄 )