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lcolladotor / biocthis

Automate package and project setup for Bioconductor packages
https://lcolladotor.github.io/biocthis/
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[BUG] Default RSPM causes workflow to fail. #41

Closed boyiguo1 closed 1 year ago

boyiguo1 commented 1 year ago

Describe the bug

The workflow generated using biocthis::use_bioc_github_action.R can fail during the Install Linux system dependencies step due to the default RSPM (https://packagemanager.rstudio.com/cran/__linux__/jammy/latest) is un available right now.

Is it possible to have a more robust source of RSPM as the default?

Provide a minimally reproducible example (reprex)

Sorry, the workflow is created as a private repo, and hence can not share with you. But I am attaching a screen print or the error page.

Screenshot 2023-05-24 at 10 26 12 AM

Here is a screen print for the default RSPM unavailable.

Screenshot 2023-05-24 at 10 26 40 AM

Expected behavior

The workflow will complete successfully.

R Session Information

The workflow is created using biocthis v1.11.1

Additional Context

The default RSPM is specified in this line https://github.com/lcolladotor/biocthis/blob/8002314df3b9fe69d7954c269d45abff9b3fed66/inst/templates/check-bioc.yml#L55

Is the package installed via bioconda?

N/A

lmweber commented 1 year ago

Seems the RStudio / Posit package managers are currently still down / unavailable -- I am still getting this error too.

I have an example of the error in this GHA run: https://github.com/lmweber/nnSVG/actions/runs/5123797666/jobs/9215096509

Also a smaller separate issue -- the package manager URL has changed to the new Posit name, from:

https://packagemanager.rstudio.com/cran/__linux__/jammy/latest

to

https://packagemanager.posit.co/cran/__linux__/jammy/latest

although both URLs are still supported for now.

lmweber commented 1 year ago

Actually I'm not sure this is due to the RSPM, because I still get the same error when I remove RSPM, e.g. in this run: https://github.com/lmweber/nnSVG/actions/runs/5124676591/jobs/9216830473

I'm not sure yet what is causing this.