Seurat v5 fix

.github/workflows/R-CMD-check.yaml

@@ -1,14 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,66 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          #- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("BiocManager")
-          BiocManager::install(update=TRUE, ask=FALSE)
-          BiocManager::install(remotes::dev_package_deps(dependencies = TRUE)[["package"]])
-          remotes::install_github("satijalab/seurat-data")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Canek
 Type: Package
 Title: Batch Correction of Single Cell Transcriptome Data
-Version: 0.2.2
+Version: 0.2.3
 Authors@R: c(
     person("Martin", "Loza", email = "martin.loza.lopez@gmail.com", role = c("aut", "cre"), 
         comment = c(ORCID = "0000-0002-3342-2643")),

README.Rmd

@@ -22,7 +22,7 @@ knitr::opts_chunk$set(
 # Canek
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/MartinLoza/Canek/workflows/R-CMD-check/badge.svg)](https://github.com/MartinLoza/Canek/actions)
+[![R-CMD-check](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Canek)](https://cran.r-project.org/package=Canek)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Canek)](https://cran.r-project.org/package=Canek)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/Canek)](https://cran.r-project.org/package=Canek)

README.md

@@ -9,7 +9,7 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/MartinLoza/Canek/workflows/R-CMD-check/badge.svg)](https://github.com/MartinLoza/Canek/actions)
+[![R-CMD-check](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Canek)](https://cran.r-project.org/package=Canek)
 [![CRAN
 Downloads](https://cranlogs.r-pkg.org/badges/Canek)](https://cran.r-project.org/package=Canek)
@@ -102,6 +102,6 @@ If you use Canek in your research please cite our work using:
 
 Loza M, Teraguchi S, Standley D, Diez D (2022). “Unbiased integration of
 single cell transcriptome replicates.” *NAR Genomics and
-Bioinformatics*, *4*(1), lqac022. doi: 10.1093/nargab/lqac022 (URL:
-<https://doi.org/10.1093/nargab/lqac022>), \<URL:
-<https://martinloza.github.io/Canek/>\>.
+Bioinformatics*, *4*(1), lqac022. <doi:10.1093/nargab/lqac022>
+<https://doi.org/10.1093/nargab/lqac022>,
+<https://martinloza.github.io/Canek/>.