add mo_pathogenicity

.github/workflows/check-old.yaml

@@ -47,7 +47,7 @@ jobs:
       matrix:
         config:
           # Test all old versions of R >= 3.0, we support them all!
-          # For these old versions, dependencies will not be installed and checked.
+          # For these old versions, dependencies and vignettes will not be checked.
           # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R versions).
           - {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
@@ -82,8 +82,8 @@ jobs:
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
-      - name: Remove vignettes on R without knitr support
-        if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3'
+      - name: Remove vignettes
+        if: always() # matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3'
         # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R <= 3.3 as writeLines() cannot overwrite
         run: |
           rm -rf vignettes
@@ -101,7 +101,7 @@ jobs:
           _R_CHECK_LENGTH_1_CONDITION_: verbose
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
           # no check for old R versions - these packages require higher R versions
-          _R_CHECK_RD_XREFS_: ${{ matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' && matrix.config.r != '3.3' && matrix.config.r != '3.4' }}
+          _R_CHECK_RD_XREFS_: false
           _R_CHECK_FORCE_SUGGESTS_: false
           R_CHECK_CONSTANTS: 5
           R_JIT_STRATEGY: 3

.github/workflows/check-recent.yaml

@@ -99,6 +99,5 @@ jobs:
       - name: Show tinytest output
         if: always()
         run: |
-          ls -lh
           find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash