diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index c919d36..7cfe6a8 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -52,9 +52,9 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: 'release', bioc: '3.19'} - # - { os: macOS-latest, r: 'devel', bioc: '3.20'} - - { os: windows-latest, r: 'release', bioc: '3.19'} + - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + #- { os: macOS-latest, r: 'next', bioc: '3.19'} + - { os: windows-latest, r: 'next', bioc: '3.19'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: @@ -191,7 +191,7 @@ jobs: gha_repos <- if( .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin" ) c( - "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.17/bioc", + "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.19/bioc", BiocManager::repositories() ) else BiocManager::repositories() @@ -205,8 +205,9 @@ jobs: BiocManager::install("mzR", force = TRUE) BiocManager::install("MSnbase", force = TRUE, type = "source") BiocManager::install("xcms", force = TRUE, type = "source", dependencies = TRUE) - - BiocManager::install(c("BiocStyle", "msPurityData", "CAMERA")) + BiocManager::install("msPurityData", force = TRUE, type = "source", dependencies = TRUE) + BiocManager::install("CAMERA", force = TRUE, type = "source", dependencies = TRUE) + BiocManager::install(c("BiocStyle")) install.packages(c("rmarkdown", "RPostgres", "RMySQL"))