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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Temporal fix for rworkflow bug #540

Closed Daenarys8 closed 1 month ago

Daenarys8 commented 2 months ago

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 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

Roxygen2 changed how list is created. It seems that it throws now a warning. This is related to this issue: https://github.com/microbiome/mia/issues/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 commented 1 month ago

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

TuomasBorman commented 1 month ago

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

Daenarys8 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

https://github.com/neurogenomics/rworkflows/issues/130

Try to put R back to auto. It should work

TuomasBorman commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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