Merge pull request #118 from rformassspectrometry/jomain

fix: missing dependency of ProtGenerics
rformassspectrometry · Oct 16, 2024 · 8f4499b · 8f4499b
2 parents b96137d + 6344dd5
commit 8f4499b
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Showing 4 changed files with 41 additions and 35 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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"))