ci: ensure packages are indeed installed from source

.github/workflows/check-bioc.yml

@@ -182,10 +182,16 @@ jobs:
  BiocManager::install("BiocParallel", force = TRUE, type = "source")
  BiocManager::install("S4Vectors", force = TRUE, type = "source")
  BiocManager::install("SummarizedExperiment", force = TRUE, type = "source")
+ ## install xcms with dependencies - to ensure dependencies are installed from source;
+ ## somehow install_local installs binary packages instead.
+ BiocManager::install("mzR", force = TRUE)
+ BiocManager::install("MSnbase", force = TRUE, type = "source")
+ BiocManager::install("xcms", force = TRUE, type = "source", dependencies = TRUE)
+ BiocManager::install("faahKO", type = "source")
 
  ## Pass #1 at installing dependencies
  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")
+ remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, build_manual = FALSE, type = "source")
 
  BiocManager::install(c("rmarkdown", "BiocStyle"), type = "source")
  continue-on-error: true
@@ -195,16 +201,12 @@ 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, force = TRUE, type = "source")
+ remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, type = "source")
 
  ## Manually install packages that seem to be skipped.
  message(paste('****', Sys.time(), 'force installation of selected packages ****'))
  BiocManager::install("RforMassSpectrometry/MsCoreUtils", force = TRUE)
- BiocManager::install("xcms", type = "source")
- BiocManager::install("faahKO", type = "source", force = TRUE)
  BiocManager::install("magick", type = "source")
- BiocManager::install("RCurl", type = "source", force = TRUE)
- BiocManager::install("mzR")
 
  ## For running the checks
  message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))

DESCRIPTION

@@ -84,8 +84,7 @@ Suggests:
  multtest,
  MsBackendMgf,
  signal,
- mgcv,
- RCurl
+ mgcv
 Enhances:
  Rgraphviz,
  rgl