GHA Docker: ` API rate limit exceeded`

[bschilder]

It looks like my GH token is not getting passed to the Dockerfile when it's run through the GHA workflow.

https://github.com/RajLabMSSM/echolocatoR/actions/runs/3369321084/jobs/5588841392#step:33:1415

Skipping install of 'echodata' from a github remote, the SHA1 (d94fe146) has not changed since last install.
  Use `force = TRUE` to force installation
* checking for file ‘/tmp/RtmpMzIvoK/remotes7397696c0/RajLabMSSM-echoconda-3904b0b/DESCRIPTION’ ... OK
* preparing ‘echoconda’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘echoconda_0.99.8.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘echoconda’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (echoconda)
Downloading GitHub repo RajLabMSSM/downloadR@HEAD
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 403.
  API rate limit exceeded for 172.173.247.2. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

  Rate limit remaining: 0/60
  Rate limit reset at: 2022-11-01 13:20:07 UTC

  To increase your GitHub API rate limit
  - Use `usethis::create_github_token()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
Execution halted
The command '/bin/sh -c Rscript -e 'options(download.file.method= "libcurl");                 if(!require("BiocManager")) install.packages("BiocManager");                 if(!require("AnVIL"))  {BiocManager::install("AnVIL", ask = FALSE)};                 AnVIL::install(c("remotes","devtools"));                 try({remotes::install_github("bergant/rapiclient")});                 bioc_ver <- BiocManager::version();                 options(repos = c(AnVIL::repositories(),                                  AnVIL = file.path("https://bioconductordocker.blob.core.windows.net/packages",bioc_ver,"bioc"),                                  CRAN = "https://cran.rstudio.com/"),                                  download.file.method = "libcurl", Ncpus = 2);                 deps <- remotes::dev_package_deps(dependencies = TRUE)$package;                 AnVIL::install(pkgs = deps,  ask = FALSE);                 deps_left <- deps[!deps %in% rownames(installed.packages())];                 if(length(deps_left)>0) devtools::install_dev_deps(dependencies = TRUE, upgrade = "never");'' returned a non-zero code: 1
Error: exit status 1
Usage:
exit status 1
  github-actions build-push [flags]

Flags:
  -h, --help   help for build-push

[bschilder]

Related: https://github.com/docker/build-push-action/issues/715

[bschilder]

resolve in latest version of rworkflows

[bschilder]

For some reason this is happening again...

https://github.com/RajLabMSSM/echolocatoR/actions/runs/3449430854/jobs/5757340886

Error: Failed to install 'unknown package' from GitHub:
  Failed to install 'echodata' from GitHub:
  HTTP error 403.
  API rate limit exceeded for 20.22.244.70. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

[eshults89]

Hi! This is happening to me currently. I really would love for this to work for current research. Can anyone help?

[bschilder]

@eshults89 this is actually a bit different from your issue, though the root cause is similar (not having the GitHub token set up)

[bschilder]

Resolved by current version of rworkflows: https://github.com/neurogenomics/rworkflows