update for github workflows

computational-metabolomics · Aug 29, 2023 · 7d701f8 · 7d701f8
1 parent 168130f
commit 7d701f8
Showing 1 changed file with 19 additions and 7 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -116,6 +116,7 @@ jobs:
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
+       ## Note some specifics here for ncdf4 - depends updated from XCMS github workflow
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
         run: |
@@ -140,8 +141,18 @@ jobs:
           ## For installing usethis's dependency gert
           brew install libgit2
 
-          ## Required for tcltk
-          brew install xquartz --cask
+          ## required for ncdf4
+          ## brew install netcdf ## Does not work as it is compiled with 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
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -160,6 +171,7 @@ jobs:
           BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
         shell: Rscript {0}
 
+
       - name: Install dependencies pass 1
         run: |
           ## Try installing the package dependencies in steps. First the local
@@ -180,6 +192,10 @@ jobs:
               BiocManager::repositories()
               ) else BiocManager::repositories()
 
+          # install suggested packages
+          BiocManager::install(c("MSnbase", "xcms", "BiocStyle", "msPurityData", "CAMERA"))
+          install.packages(c("rmarkdown", "RPostgres", "RMySQL"))
+
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
           install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
@@ -221,11 +237,7 @@ jobs:
           remotes::install_github("r-lib/pkgdown")
         shell: Rscript {0}
 
-      - name: Install suggested packages
-        run: |
-          BiocManager::install(c("MSnbase", "xcms", "BiocStyle", "msPurityData", "CAMERA"))
-          install.packages(c("rmarkdown", "RPostgres", "RMySQL"))
-        shell: Rscript {0}
+
 
       - name: Session info
         run: |