ci: install packages from source

sneumann · Apr 2, 2024 · f2f4475 · f2f4475
1 parent 8fb8525
commit f2f4475
Showing 1 changed file with 2 additions and 10 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -186,8 +186,7 @@ jobs:
  BiocManager::install("RforMassSpectrometry/MsCoreUtils")
  BiocManager::install(c("ncdf4", "mzR"))
  message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
- remotes::install_local(dependencies = TRUE, repos =
- BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+ remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, type = "source")
 
  BiocManager::install(c("rmarkdown", "BiocStyle"))
  continue-on-error: true
@@ -197,19 +196,12 @@ jobs:
  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 = FALSE, upgrade = TRUE)
+ remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, type = "source")
 
  ## Manually install packages that seem to be skipped.
  message(paste('****', Sys.time(), 'force installation of selected packages ****'))
  BiocManager::install(c("faahKO"))
- BiocManager::install("ProtGenerics")
- BiocManager::install("MSnbase")
- BiocManager::install("mzR", type = "source", force = TRUE)
- BiocManager::install("Spectra")
- BiocManager::install("MsBackendMgf")
- BiocManager::install("MetaboCoreUtils")
  BiocManager::install("magick")
- BiocManager::install("RforMassSpectrometry/MsExperiment")
 
  ## For running the checks
  message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))