# test r-devel

.github/workflows/check-bioc.yml

@@ -54,9 +54,10 @@ 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: '3.16'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          #- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          #- { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          #- { os: windows-latest, r: '4.4', bioc: '3.19'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -107,16 +108,20 @@ 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_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-DEVEL-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          #restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-DEVEL-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_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-DEVEL-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          #restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-DEVEL-r-4.4-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -305,7 +310,8 @@ 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_19-r-4.4-results
+          name: ${{ runner.os }}-biocversion-DEVEL-r-4.4-results
           path: check
 
 

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: r-base:4.3.2
+image: r-devel:latest
 
 before_script:
   - apt-get update

R/rbh2kaks.R

@@ -41,7 +41,7 @@
 #' @importFrom Biostrings DNAString DNAStringSet AAString AAStringSet
 #' readDNAStringSet readAAStringSet writeXStringSet width subseq
 #' @importFrom stringr word
-#' @importFrom MSA2dist dnastring2kaks cds2codonaln
+#' @importFrom MSA2dist dnastring2kaks cds2codonaln indices2kaks
 #' @seealso \code{\link[MSA2dist]{dnastring2kaks}},
 #' \code{\link[CRBHits]{isoform2longest}},
 #' \code{\link[CRBHits]{cds2genepos}},