FIx GHA issues

[bschilder]

This PR is following up on #10
to resolve any remaining issues with GitHub Actions, and to add my name to the list of contributors.

[bschilder]

Ok, so even after switching to using my GH PAT (PAT_GITHUB2), there is an issue installing gchromVAR @fl-yu
Let me look at the DESCRIPTION and make sure everything is in order there.

https://github.com/sankaranlab/SCAVENGE/actions/runs/3960552385/jobs/6784854560#step:2:583

	/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmp2Ewu53/downloaded_packages
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  cannot open URL 'https://api.github.com/repos/caleblareau/gchromVAR/contents/DESCRIPTION?ref=HEAD'
Calls: saveRDS ... github_DESCRIPTION -> download -> base_download -> base_download_headers
Execution halted

[bschilder]

Ok, so I check gchromVAR and the DESCRIPTION seems to be fine. Also confirmed that i can download the package with:

devtools::install_github("caleblareau/gchromVAR", force = TRUE)

However I did notice some messages during installation:

Using github PAT from envvar GITHUB_TOKEN
Downloading GitHub repo caleblareau/gchromVAR@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/RtmpIGoWjO/remotes3755a8b606f/caleblareau-gchromVAR-e4f33ca/DESCRIPTION’ ...
─  preparing ‘gchromVAR’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘gchromVAR_0.3.2.tar.gz’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-4_0bda2f6964cc325e83aac64c4b479753.RData’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-4_0bda2f6964cc325e83aac64c4b479753.rdb’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-4_0bda2f6964cc325e83aac64c4b479753.rdx’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-5_c5bce9ef8b386761f85136789642e6fb.RData’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-5_c5bce9ef8b386761f85136789642e6fb.rdb’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-5_c5bce9ef8b386761f85136789642e6fb.rdx’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-6_e1420283e6bfd55d637fa07935427384.RData’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-6_e1420283e6bfd55d637fa07935427384.rdb’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-6_e1420283e6bfd55d637fa07935427384.rdx’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-7_8b8374748c3913f1698f2c4fde2a7661.RData’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-7_8b8374748c3913f1698f2c4fde2a7661.rdb’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-7_8b8374748c3913f1698f2c4fde2a7661.rdx’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-8_6373f14e60302c88800d9a8c00e71628.RData’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-8_6373f14e60302c88800d9a8c00e71628.rdb’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘gchromVAR/vignettes/gchromVAR_vignette_cache/html/unnamed-chunk-8_6373f14e60302c88800d9a8c00e71628.rdx’
   
* installing *source* package ‘gchromVAR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gchromVAR)
Adding ‘gchromVAR_0.3.2.tgz’ to the cache

Wondering if these storing paths of more than 100 bytes is not portable: files are related?

Originally, I was able to pass all GHA runs on neurogenomics/SCAVENGE. But now i see the same errors as sankaranlab/SCAVENGE. The only way I can explain this is that something changed in between my first PR and when the PR was merged.
https://github.com/neurogenomics/SCAVENGE/actions/runs/3960552155/jobs/6784854032#step:2:587

I'd say it's something in gchromVAR, but nothing has been changed in 3-5 years!
Unless there's something in the repo settings that prevent GHA from installing it.
@caleblareau do you have any insights here? Apologies in advance if turns out this is unrelated to gchromVAR!

https://github.com/caleblareau/gchromVAR

[bschilder]

Actually, nvm about being able to download gchromVAR , seems to working fine on my fork. It was only failing bc I don't have a secret named PAT_GITHUB2 in that repo.
https://github.com/neurogenomics/SCAVENGE/actions/runs/3960787664/jobs/6785393663

A thought just occurred to me: @fl-yu are you registered as a member of the sankaranlab GitHub org?
On the right I noticed it says "This organization has no public members." Since these seems to be a permissions issue, im wondering if that's the source.
https://github.com/sankaranlab

[fl-yu]

Thank you Brian for working on this. I think I was a member of https://github.com/sankaranlab, but I am not sure if I was a public member. How can I confirm that?

[bschilder]

Thank you Brian for working on this. I think I was a member of https://github.com/sankaranlab, but I am not sure if I was a public member. How can I confirm that?

I don't know off the top of my head but I'm sure you can find out with a bit of searching. You could also try asking someone who is an admin of sankaranlab to check your permissions.

[fl-yu]

I just set myself public while it still does not work. I wonder if this is possibly the case. actions/upload-artifact#232

[bschilder]

I just set myself public while it still does not work.

I don't think public/private matters in this case, but what permissions you've been granted does. Can you check this?

I wonder if this is possibly the case. actions/upload-artifact#232

upload-artifact is triggered right after any process fails. So while it may indeed not be uploading the bug report properly (according to the warning message), I don't believe this is the source of the error. Thanks for sharing though!

[bschilder]

Hey @fl-yu , just checked up on this and it seems that SCAVENGE is getting through all steps except the very last one on Linux when trying to push to DockerHub:
https://github.com/sankaranlab/SCAVENGE/actions/runs/4206962076/jobs/7301128788#step:5:8797

It says something is up with the login/password credentials. Can you double check that:

1. The GH Secret DOCKER_TOKEN is correct.
2. After logging into DockerHub, make sure your token has the correct write permissions.

[fl-yu]

Hey @fl-yu , just checked up on this and it seems that SCAVENGE is getting through all steps except the very last one on Linux when trying to push to DockerHub: https://github.com/sankaranlab/SCAVENGE/actions/runs/4206962076/jobs/7301128788#step:5:8797

It says something is up with the login/password credentials. Can you double check that:

1. The GH Secret DOCKER_TOKEN is correct.
2. After logging into DockerHub, make sure your token has the correct write permissions.

Hooray Brian, this is awesome! I can visit the get started page now https://sankaranlab.github.io/SCAVENGE/articles/SCAVENGE.
I will check on these. Thank you! Just wondering what magic you use

[bschilder]

hey @fl-yu just wanted to check in and see if you managed to get the Docker token permissions working?

[codecov-commenter]

Codecov Report

❗ No coverage uploaded for pull request base (main@e1bb5b4). Click here to learn what that means.
Patch has no changes to coverable lines.

❗ Current head 0db4bb7 differs from pull request most recent head 0616eda. Consider uploading reports for the commit 0616eda to get more accurate results

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Additional details and impacted files

@@          Coverage Diff           @@
##             main     #12   +/-   ##
======================================
  Coverage        ?   0.00%           
======================================
  Files           ?      11           
  Lines           ?     181           
  Branches        ?       0           
======================================
  Hits            ?       0           
  Misses          ?     181           
  Partials        ?       0           

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[bschilder]

Still seems to be some scoping issues at the Org level for the GITHUB_TOKEN variable. See here for a similar scenario:
ad-m/github-push-action#96