Temporal fix for rworkflow bug

[Daenarys8]

This commit provides a temporal fix to rworkflow by bumping the r version of MacOS and Ubuntu and
fixing a bug in R/estimateDiversity.R.

[Daenarys8]

Bumping r version for Mac workflow tends to work. I think the same for Ubuntu at least, until the fix in
R/estimateDiversity.R is merged.

[TuomasBorman]

Alright, maybe we could go like this as a temporary fix. Can you fix estimateDiversity.R in this PR (change the title also according to that)

[TuomasBorman]

Roxygen2 changed how list is created. It seems that it throws now a warning. This is related to this issue: #532

Check the workflow run, you will see these warnings:

 Warning in readLines(conn, line - oldline, warn = FALSE) :
    invalid input found on input connection './man/estimateDominance.Rd'
  checkRd: (-1) estimateDominance.Rd:99-101: Lost braces in \itemize; meant \describe ?

Can you fix them?

See for example from here how lists are now created

[Daenarys8]

@TuomasBorman I think we can finalize this now. Unless, you have more changes in mind

[TuomasBorman]

Looks good, but still not working. Update manual pages, let's see if that works

[Daenarys8]

I updated man pages already. The fail is as at the stage of deployment. Something about the bot not having permission to deploy to the repo. See log here

[TuomasBorman]

Now there is another error. Can you remove the rworkflows file and then create a new one with rworkflows::use_workflow(). That should update the workflow. Remember to specify R version to 4.4.0 (auto seems not to work)

In the future, create branch directly to mia. It is simpler since then I can also contribute much easier.

[TuomasBorman]

neurogenomics/rworkflows#130

Try to put R back to auto. It should work

[TuomasBorman]

From the rworkflows issue

One thing that might help is removing the ubuntu-latest rspm line, or replacing it with rspm: ~

Can you try that fix?

[Daenarys8]

From the rworkflows issue

One thing that might help is removing the ubuntu-latest rspm line, or replacing it with rspm: ~

Can you try that fix?

Yeah, I tried this. Still failing. I think the issue here is permission to microbiome/mia.git is denied to github-actions[bot]. I'm not quite sure but did we alter the secrets?

[TuomasBorman]

From the rworkflows issue

One thing that might help is removing the ubuntu-latest rspm line, or replacing it with rspm: ~

Can you try that fix?

Yeah, I tried this. Still failing. I think the issue here is permission to microbiome/mia.git is denied to github-actions[bot]. I'm not quite sure but did we alter the secrets?

Yes, I noticed that too. However, nothing should have changed. I will check