Merge branch 'devel' of github.com:LieberInstitute/slurmjobs into devel

LieberInstitute · Jan 6, 2025 · 64e978c · 64e978c
2 parents ea14811 + 2b9e8dc
commit 64e978c
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -105,16 +105,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-
 
       # - name: Install Linux system dependencies
       #   if: runner.os == 'Linux'
@@ -253,7 +253,7 @@ jobs:
       - name: Test coverage
         if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
-          covr::codecov()
+          covr::codecov(coverage = covr::package_coverage(type = "all"))
         shell: Rscript {0}
 
       - name: Install package
@@ -286,7 +286,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-results
           path: check
 
 

diff --git a/README.Rmd b/README.Rmd
@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/slurmjobs)](https://github.com/LieberInstitute/slurmjobs/issues)
 [![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/slurmjobs)](https://github.com/LieberInstitute/slurmjobs/pulls)
-[![R-CMD-check-bioc](https://github.com/LieberInstitute/slurmjobs/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/slurmjobs/actions/workflows/check-bioc.yml)
+[![R-CMD-check-bioc](https://github.com/LieberInstitute/slurmjobs/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/slurmjobs/actions/workflows/check-bioc.yml)
 [![Codecov test coverage](https://codecov.io/gh/LieberInstitute/slurmjobs/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/LieberInstitute/slurmjobs?branch=devel)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 <!-- badges: end -->

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 issues](https://img.shields.io/github/issues/LieberInstitute/slurmjobs)](https://github.com/LieberInstitute/slurmjobs/issues)
 [![GitHub
 pulls](https://img.shields.io/github/issues-pr/LieberInstitute/slurmjobs)](https://github.com/LieberInstitute/slurmjobs/pulls)
-[![R-CMD-check-bioc](https://github.com/LieberInstitute/slurmjobs/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/slurmjobs/actions/workflows/check-bioc.yml)
+[![R-CMD-check-bioc](https://github.com/LieberInstitute/slurmjobs/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/slurmjobs/actions/workflows/check-bioc.yml)
 [![Codecov test
 coverage](https://codecov.io/gh/LieberInstitute/slurmjobs/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/LieberInstitute/slurmjobs?branch=devel)
 [![Lifecycle: