Bioc devel

.github/workflows/check-bioc.yml

@@ -53,10 +53,10 @@ jobs:
       matrix:
         config:
           # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. 
-          - { 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: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
+          - { 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:devel",        rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest,   r: '4.3',  bioc: '3.18'}
+          - { os: windows-latest, r: '4.3',  bioc: '3.18'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -107,16 +107,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
+          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
 
       - 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-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
+          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -314,7 +314,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results
+          name: ${{ matrix.config.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results
           path: check
 
         ## Note that DOCKER_PASSWORD is really a token for your dockerhub

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: OUTRIDER
 Title: OUTRIDER - OUTlier in RNA-Seq fInDER
 Type: Package
-Version: 1.20.1
+Version: 1.21.3
 Date: 2024-04-24
 URL: https://github.com/gagneurlab/OUTRIDER
-BugRepots: https://github.com/gagneurlab/OUTRIDER/issues
+BugReports: https://github.com/gagneurlab/OUTRIDER/issues
 Authors@R: c(
     person("Felix", "Brechtmann", role=c("aut"), 
             email="[email protected]"),
@@ -27,7 +27,7 @@ biocViews: ImmunoOncology, RNASeq, Transcriptomics, Alignment, Sequencing,
 License: MIT + file LICENSE
 NeedsCompilation: yes
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends:
     R (>= 3.6), 
     BiocParallel,
@@ -59,6 +59,7 @@ Imports:
     scales,
     splines,
     stats,
+    txdbmaker,
     utils
 Suggests: 
     testthat,

NAMESPACE

@@ -96,7 +96,6 @@ importFrom(DESeq2,replaceOutliers)
 importFrom(DESeq2,show)
 importFrom(DESeq2,sizeFactors)
 importFrom(GenomicFeatures,exonsBy)
-importFrom(GenomicFeatures,makeTxDbFromGFF)
 importFrom(GenomicRanges,GRanges)
 importFrom(GenomicRanges,end)
 importFrom(GenomicRanges,findOverlaps)
@@ -217,6 +216,7 @@ importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,var)
+importFrom(txdbmaker,makeTxDbFromGFF)
 importFrom(utils,compareVersion)
 importFrom(utils,head)
 importFrom(utils,packageVersion)

NEWS

@@ -1,4 +1,4 @@
-CHANGES IN VERSION 1.20.1
+CHANGES IN VERSION 1.22.0
 -----------------------------
     o Add Manhattenplot functionallity
     o Bugfix in restricting for FDR correction and others (#54 and aa6e56a)

R/package-OUTRIDER.R

@@ -26,7 +26,9 @@
 #' @importFrom BiocParallel bplapply bpparam SerialParam bpisup bpstart bpstop
 #'          bpmapply
 #' 
-#' @importFrom GenomicFeatures makeTxDbFromGFF exonsBy
+#' @importFrom GenomicFeatures exonsBy
+#' 
+#' @importFrom txdbmaker makeTxDbFromGFF
 #' 
 #' @importFrom GenomicRanges GRanges reduce width start end findOverlaps 
 #' 

README.md

@@ -47,7 +47,7 @@ install.packages('devtools')
 devtools::install_github('gagneurlab/OUTRIDER', dependencies=TRUE)
 
 # installing a specific version/tag of OUTRIDER
-devtools::install_github('gagneurlab/OUTRIDER@1.20.1', dependencies=TRUE)
+devtools::install_github('gagneurlab/OUTRIDER@1.22.0', dependencies=TRUE)
 ```
 
 To check which versions/tags are available you can check the GitHub repo