diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 43614b7..f6f4a41 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -53,7 +53,7 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { 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: '4.4', bioc: '3.20'} - { os: windows-latest, r: '4.4', bioc: '3.20'} env: @@ -124,31 +124,32 @@ jobs: - name: Install macOS system dependencies if: matrix.config.os == 'macOS-latest' run: | - ## Enable installing XML from source if needed - brew install libxml2 - echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV - - ## Required to install magick as noted at - ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 - brew install imagemagick@6 - - ## For textshaping, required by ragg, and required by pkgdown - brew install harfbuzz fribidi - - ## For installing usethis's dependency gert - brew install libgit2 - - ## required for ncdf4 - can not use the homebrew one because that uses GCC - ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/ - curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz - tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C / - rm netcdf-4.7.4-darwin.17-x86_64.tar.gz - curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz - tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C / - rm hdf5-1.12.0-darwin.17-x86_64.tar.gz - curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz - tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C / - rm szip-2.1.1-darwin.17-x86_64.tar.gz + # ## Enable installing XML from source if needed + # brew install libxml2 + # echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV + + # ## Required to install magick as noted at + # ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 + # brew install imagemagick@6 + + # ## For textshaping, required by ragg, and required by pkgdown + # brew install harfbuzz fribidi + + # ## For installing usethis's dependency gert + # brew install libgit2 + + # ## required for ncdf4 - can not use the homebrew one because that uses GCC + # ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/ + # curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz + # tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C / + # rm netcdf-4.7.4-darwin.17-x86_64.tar.gz + # curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz + # tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C / + # rm hdf5-1.12.0-darwin.17-x86_64.tar.gz + # curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz + # tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C / + # rm szip-2.1.1-darwin.17-x86_64.tar.gz + shell: Rscript {0} - name: Install Windows system dependencies if: runner.os == 'Windows' @@ -196,12 +197,12 @@ jobs: remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) ## Manually install required packages - BiocManager::install('rhdf5', dependencies = TRUE, ask = FALSE, update = FALSE, INSTALL_opts = '--force-biarch') - BiocManager::install("mzR", dependencies = TRUE, ask = FALSE, update = FALSE) - BiocManager::install("msdata") - BiocManager::install("HenrikBengtsson/matrixStats") - BiocManager::install("SummarizedExperiment", dependencies = TRUE, ask = FALSE, update = FALSE) - BiocManager::install("QFeatures", dependencies = TRUE, ask = FALSE, update = FALSE) + # BiocManager::install('rhdf5', dependencies = TRUE, ask = FALSE, update = FALSE, INSTALL_opts = '--force-biarch') + # BiocManager::install("mzR", dependencies = TRUE, ask = FALSE, update = FALSE) + # BiocManager::install("msdata") + # BiocManager::install("HenrikBengtsson/matrixStats") + # BiocManager::install("SummarizedExperiment", dependencies = TRUE, ask = FALSE, update = FALSE) + # BiocManager::install("QFeatures", dependencies = TRUE, ask = FALSE, update = FALSE) BiocManager::install("AnnotationHub", dependencies = TRUE, ask = FALSE, update = FALSE) BiocManager::install("RforMassSpectrometry/CompoundDb") library(AnnotationHub) @@ -282,7 +283,7 @@ jobs: - name: Test coverage if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux' run: | - covr::codecov() + covr::codecov(token = "{{ secrets.CODECOV_TOKEN }}") shell: Rscript {0} - name: Install package diff --git a/DESCRIPTION b/DESCRIPTION index 84d2e5f..dbae4ad 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MetaboAnnotation Title: Utilities for Annotation of Metabolomics Data -Version: 1.9.1 +Version: 1.9.2 Description: High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on @@ -70,7 +70,7 @@ BugReports: https://github.com/RforMassSpectrometry/MetaboAnnotation/issues URL: https://github.com/RforMassSpectrometry/MetaboAnnotation biocViews: Infrastructure, Metabolomics, MassSpectrometry Roxygen: list(markdown=TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Collate: 'AllClassUnions.R' 'AllGenerics.R' diff --git a/NEWS.md b/NEWS.md index f12d0e1..9255bfa 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # MetaboAnnotation 1.9 +## Changes in 1.9.2 + +- Fix missing ProtGenerics dependency. + ## Changes in 1.9.1 - Add parameter `scalePeaks` to `plotSpectraMirror` to allow scaling peak diff --git a/tests/testthat/test_MatchedSpectra.R b/tests/testthat/test_MatchedSpectra.R index dcbd54d..632a5e7 100644 --- a/tests/testthat/test_MatchedSpectra.R +++ b/tests/testthat/test_MatchedSpectra.R @@ -1,4 +1,5 @@ library(Spectra) +library(ProtGenerics) df1 <- DataFrame( msLevel = 2L, rtime = 1:10, spectrum_id = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j"))