Updating check-bioc GHA
#11
Conversation
renew `biocthis::use_bioc_github_action()`
Remove parts not used (yet)
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Ok this is great ! Actually the checks will not be able to pass if the vignettes are run because Sirius cannot be installed/run in the GHA (that i know of). My thought was to do them once the docker image (with Sirius installed there) is created ! because then i can run the check on the docker image. So i think for now it's good enough. What we can try is to just not build vignette for now also. and I will turn that back on once the Docker image is ready. |
| ## Manually install required packages | ||
| BiocManager::install("msdata") | ||
| BiocManager::install("msentropy") # NOTE: not because of `RuSirius` but `Spectra` |
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it's super weird this is not automatically installed, i will signal to jo
.github/workflows/check-bioc.yml
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| run: | | ||
| ## Pass #2 at installing dependencies | ||
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) |
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maybe for now we change this to build_vignettes = FALSE and I'll fix all of that when I have the docker.
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Changed it, removed all vignettes builds, which leads to 2 warnings (out of 3, an additional other one remains...): https://github.com/rformassspectrometry/RuSirius/actions/runs/12908258406/job/35993408675#step:20:129
| ## NOTE: Change this back when everything ready | ||
| # build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | ||
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data", "--no-build-vignettes"), | ||
| error_on = "warning", |
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No need to throw error on warnings for now i think. the warning we get are just related to the fact that we are not building the vignettes.
Let's remove this and merge the PR. and i'll look more into it with the docker !
@philouail
Sadly still not passing but already goes further than before and allowed probably to catch a real "error"!
NOTEon things that should be modified later