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sankaranlab / SCAVENGE

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
GNU General Public License v3.0
79 stars 34 forks source link

FIx GHA issues #12

Open bschilder opened 1 year ago

bschilder commented 1 year ago

This PR is following up on https://github.com/sankaranlab/SCAVENGE/pull/10 to resolve any remaining issues with GitHub Actions, and to add my name to the list of contributors.

bschilder commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

bschilder commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

codecov-commenter commented 1 year ago

Codecov Report

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

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

:exclamation: Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the GitHub App Integration for your organization. Read more.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #12 +/- ## ====================================== Coverage ? 0.00% ====================================== Files ? 11 Lines ? 181 Branches ? 0 ====================================== Hits ? 0 Misses ? 181 Partials ? 0 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

bschilder commented 1 year ago

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