diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 25c1961..5d57639 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -52,15 +52,16 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } # Skip other OSes for now -# - { os: macOS-latest, r: 'devel', bioc: '3.17'} -# - { os: windows-latest, r: 'devel', bioc: '3.17'} +# - { os: macOS-latest, r: '4.3', bioc: '3.18'} +# - { os: windows-latest, r: '4.3', bioc: '3.18'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} NOT_CRAN: true +# NOT_CRAN: false TZ: UTC VDIFFR_RUN_TESTS: false GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -73,8 +74,9 @@ jobs: - name: Set R Library home on Linux if: runner.os == 'Linux' run: | - mkdir /__w/_temp/Library + mkdir -p /__w/_temp/Library echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile + sudo -s eval "apt-get update -y && apt-get install -y nodejs" ## Most of these steps are the same as the ones in ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml @@ -97,7 +99,7 @@ jobs: - name: Query dependencies run: | install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + #saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} - name: Cache R packages @@ -235,7 +237,7 @@ jobs: rcmdcheck::rcmdcheck( args = c("--no-build-vignettes", "--no-manual", "--timings"), build_args = c("--no-manual", "--no-resave-data"), - error_on = "warning", + error_on = "error", check_dir = "check" ) shell: Rscript {0} diff --git a/DESCRIPTION b/DESCRIPTION index 39ab432..12a2877 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,27 +20,28 @@ Authors@R: c( ) Maintainer: Steffen Neumann Description: MetClassNetR collects a tool set for integrating metabolomics data as a network system. +BiocViews: MassSpectrometry Depends: igraph (>= 1.3.0), - MetNet (>= 1.14.0), MsCoreUtils, - MSnbase, mpmi, - QFeatures, - nontarget + QFeatures Imports: ggplot2, methods, + MetNet (>= 1.14.0), + MSnbase, MsBackendMgf, QFeatures, plyr, RCy3, readr, Spectra, - UpSetR + UpSetR, + dplyr, + stringr Suggests: BiocStyle (>= 2.5.19), - dplyr, ggrepel, grid, knitr (>= 1.1.0), @@ -56,7 +57,8 @@ Suggests: Remotes: sneumann/MsBackendMsp, aberHRML/classyfireR, - CDK-R/rinchi + CDK-R/rinchi, + blosloos/nontarget License: Artistic-2.0 Encoding: UTF-8 Roxygen: list(markdown = TRUE)