ci: install all packages from source

.github/workflows/check-bioc.yml

@@ -160,12 +160,12 @@ jobs:
  - name: Install BiocManager
  run: |
  message(paste('****', Sys.time(), 'installing BiocManager ****'))
- remotes::install_cran("BiocManager")
+ remotes::install_cran("BiocManager", type = "source")
  shell: Rscript {0}
 
  - name: Set BiocVersion
  run: |
- BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+ BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, type = "source")
  shell: Rscript {0}
 
  - name: Install dependencies pass 1
@@ -186,7 +186,7 @@ jobs:
  message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
  remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, force = TRUE, type = "source")
 
- BiocManager::install(c("rmarkdown", "BiocStyle"))
+ BiocManager::install(c("rmarkdown", "BiocStyle"), type = "source")
  continue-on-error: true
  shell: Rscript {0}
 
@@ -201,19 +201,19 @@ jobs:
  BiocManager::install("RforMassSpectrometry/MsCoreUtils", force = TRUE)
  BiocManager::install("xcms", type = "source")
  BiocManager::install("faahKO", type = "source", force = TRUE)
- BiocManager::install("magick")
+ BiocManager::install("magick", type = "source")
 
  ## For running the checks
  message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
- remotes::install_cran("rcmdcheck")
- BiocManager::install(c("BiocCheck", "DBI"))
+ remotes::install_cran("rcmdcheck", type = "source")
+ BiocManager::install("BiocCheck", type = "source")
  shell: Rscript {0}
 
  - name: Install BiocGenerics
  if: env.has_RUnit == 'true'
  run: |
  ## Install BiocGenerics
- BiocManager::install("BiocGenerics")
+ BiocManager::install("BiocGenerics", type = "source")
  shell: Rscript {0}
 
  - name: Install covr