new package cache issue

[diazrenata]

https://github.com/role-model/multidim-biodiv-data/actions/runs/4325512170/jobs/7551764452#logs

Fortify local {renv} packages
  ℹ Consent to use package cache provided
  → Searching for and installing available dependencies
  Finding R package dependencies ... Done!
  * Discovering package dependencies ... Done!
  The following packages were discovered:
  
  # ~/work/_temp/Library ===============
  - R6          2.5.1
  - base64enc   0.1-3
  - bslib       0.4.2
  - cachem      1.0.7
  - cli         3.6.0
  - digest      0.6.31
  - ellipsis    0.3.2
  - evaluate    0.20
  - fastmap     1.1.1
  - fs          1.6.1
  - glue        1.6.2
  - highr       0.10
  - htmltools   0.5.4
  - jquerylib   0.1.4
  - jsonlite    1.8.4
  - knitr       1.42
  - lifecycle   1.0.3
  - magrittr    2.0.3
  - memoise     2.0.1
  - mime        0.12
  - rappdirs    0.3.3
  - rlang       1.0.6
  - rmarkdown   2.20
  - sass        0.4.5
  - stringi     1.7.12
  - stringr     1.5.0
  - tinytex     0.44
  - vctrs       0.5.2
  - xfun        0.37
  - yaml        2.3.7
  
  They will be linked into the project library.
  
  * Linking packages into the project library ... The following packages are used in this project, but not available locally:
  
  	dplyr, ggplot2, hillR, taxize, tidyr, vegan
  
  renv will attempt to download and install these packages.
  
  Done!
  * Hydrated 30 packages in 0.14 seconds.
  * Resolving missing dependencies  ... 
  The following package(s) were not installed successfully:
  
  	[hillR]: object of type 'promise' is not subsettable
  	[dplyr]: object of type 'promise' is not subsettable
  	[vegan]: object of type 'promise' is not subsettable
  	[taxize]: object of type 'promise' is not subsettable
  	[tidyr]: object of type 'promise' is not subsettable
  	[ggplot2]: object of type 'promise' is not subsettable
  
  You may need to manually download and install these packages.
  
  ! Attempting to install missing packages assuming bioc
  There were 36 warnings (use warnings() to see them)
  Error: 
  ! in callr subprocess.
  Caused by error in `loadNamespace(name)`:
  ! there is no package called ‘BiocManager’
  ---
  Standard output:
  Finding R package dependencies ... Done!
  * Discovering package dependencies ... Done!
  * Linking packages into the project library ... Done!
  * Hydrated 30 packages in 0.14 seconds.
  * Resolving missing dependencies  ...
  ---
  Standard error:
  → Searching for and installing available dependencies
  The following packages were discovered:
  
  # ~/work/_temp/Library ===============
  - R6          2.5.1
  - base64enc   0.1-3
  - bslib       0.4.2
  - cachem      1.0.7
  - cli         3.6.0
  - digest      0.6.31
  - ellipsis    0.3.2
  - evaluate    0.20
  - fastmap     1.1.1
  - fs          1.6.1
  - glue        1.6.2
  - highr       0.10
  - htmltools   0.5.4
  - jquerylib   0.1.4
  - jsonlite    1.8.4
  - knitr       1.42
  - lifecycle   1.0.3
  - magrittr    2.0.3
  - memoise     2.0.1
  - mime        0.12
  - rappdirs    0.3.3
  - rlang       1.0.6
  - rmarkdown   2.20
  - sass        0.4.5
  - stringi     1.7.12
  - stringr     1.5.0
  - tinytex     0.44
  - vctrs       0.5.2
  - xfun        0.37
  - yaml        2.3.7
  
  They will be linked into the project library.
  
  The following packages are used in this project, but not available locally:
  
  	dplyr, ggplot2, hillR, taxize, tidyr, vegan
  
  renv will attempt to download and install these packages.
  
  The following package(s) were not installed successfully:
  
  	[hillR]: object of type 'promise' is not subsettable
  	[dplyr]: object of type 'promise' is not subsettable
  	[vegan]: object of type 'promise' is not subsettable
  	[taxize]: object of type 'promise' is not subsettable
  	[tidyr]: object of type 'promise' is not subsettable
  	[ggplot2]: object of type 'promise' is not subsettable
  
  You may need to manually download and install these packages.
  
  ! Attempting to install missing packages assuming bioc
  There were 36 warnings (use warnings() to see them)
  ---
  Backtrace:
  1. sandpaper::manage_deps(path = wd, quiet = FALSE)
  2. callr::r(func = callr_manage_deps, args = args, show = !quiet, …
  3. callr:::get_result(output = out, options)
  4. callr:::throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
  ---
  Subprocess backtrace:
   1. renv::install(paste0("bioc::", pkgs), library = renv_lib, project = path)
   2. renv:::retrieve(names(remotes))
   3. local handler(package, renv_retrieve_impl(package))
   4. renv:::renv_retrieve_impl(package)
   5. renv:::renv_scope_bioconductor(project = project)
   6. renv:::renv_bioconductor_repos(project = project, version = version)
   7. renv:::renv_bioconductor_repos_biocmanager(version)
   8. base::asNamespace("BiocManager")
   9. base::getNamespace(ns)
  10. base::loadNamespace(name)
  11. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  12. base::withOneRestart(expr, restarts[[1L]])
  13. base::doWithOneRestart(return(expr), restart)
  14. base::stop(cond)
  15. global (function (e) …
  Execution halted
  Error: Process completed with exit code 1.

Current workaround for the purposes of having a site that builds today at 1:

• Changed github pages to build from the 'docs' dir on main
• Deleted the build and deploy site action
• Ran sandpaper::build_lesson locally
• Copied the contents of the locally build site/docs dir to docs
• Removed docs/ from .gitignore

This isn't sustainable, but it works for now.

[zkamvar]

Hello,

You happened to run into the unfortunate situation of being in the wrong place at the wrong time.

This was a particularly nasty bug coming from a dependency of {sandpaper} that updated two weeks ago (see carpentries/sandpaper#406). It has since been patched and should work now.

[zkamvar]

My suggestion would be to locally run:

sandpaper::update_github_workflows() # update the workflows
sandpaper::manage_deps() 
sandpaper::update_cache() # update the package cache

I would recommend setting up a bot to create pull requests that will keep your repo up to date periodically: https://carpentries.github.io/sandpaper/articles/automated-pull-requests.html