From b52457ae41319d08082cedac2e243a52f6fa0c17 Mon Sep 17 00:00:00 2001 From: jorainer Date: Tue, 2 Apr 2024 16:48:24 +0200 Subject: [PATCH] ci: install all packages from source --- .github/workflows/check-bioc.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index a573c9dc1..1b389dc59 100644 --- a/.github/workflows/check-bioc.yml +++ b/.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