Merge branch 'devel' of git.bioconductor.org:packages/tximeta into devel

thelovelab · Sep 27, 2024 · e91175a · e91175a
2 parents a358e7b + ccf9675
commit e91175a
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Showing 4 changed files with 12 additions and 11 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -54,7 +54,7 @@ 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__/focal/latest" }
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -106,16 +106,16 @@ jobs:
         uses: actions/cache@v2
         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') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v2
         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') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -270,7 +270,7 @@ 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_19-r-4.4-results
           path: check
 
       - uses: docker/build-push-action@v1

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: tximeta
-Version: 1.23.1
+Version: 1.23.2
 Title: Transcript Quantification Import with Automatic Metadata
 Description: Transcript quantification import from Salmon and
     other quantifiers with automatic attachment of transcript ranges

diff --git a/R/summarizeToGene.R b/R/summarizeToGene.R
@@ -50,9 +50,11 @@ summarizeToGene.SummarizedExperiment <- function(object,
 
   # note here about how ranges are assigned
   if (assignRanges == "abundant") {
-    message("gene ranges assigned by isoform abundance, see `assignRanges`")
+    message("assignRanges='abundant': gene ranges assigned by isoform abundance
+  see details at: ?summarizeToGene,SummarizedExperiment-method")
   } else {
-    message("gene ranges assigned by total range of isoforms, see `assignRanges`")
+    message("assignRanges='range': gene ranges assigned by total range of isoforms
+  see details at: ?summarizeToGene,SummarizedExperiment-method")
   }
 
   txi.gene <- summarizeToGene(object=txi, tx2gene=tx2gene, varReduce=varReduce, ...)

diff --git a/R/tximeta.R b/R/tximeta.R
@@ -47,11 +47,10 @@
 #'
 #' @author Michael I. Love, Charlotte Soneson, Peter Hickey, Rob Patro
 #' 
-#' @docType package
 #' @name tximeta-package
 #' @aliases tximeta-package
 #' @keywords package
-NULL
+"_PACKAGE"
 
 #' Import transcript quantification with metadata
 #'