Changed actions to 3.19

.github/workflows/check-bioc.yml

@@ -37,7 +37,7 @@ env:
   has_testthat: 'true'
   run_covr: 'true'
   run_pkgdown: 'true'
-  cache-version: 'cache-v3'
+  cache-version: 'cache-v1'
   run_docker: 'false'
 
 jobs:
@@ -51,9 +51,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.4', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", 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: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          - { os: windows-latest, r: '4.4', bioc: '3.19'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -101,16 +101,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-next-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-next-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-3.19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-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@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-next-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-next-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-3.19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-3.19-r-4.4-
 
 
       - name: Install macOS system dependencies
@@ -267,7 +267,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-devel-r-next-results
+          name: ${{ runner.os }}-biocversion-3.19-r-4.4-results
           path: check
 
       - uses: docker/build-push-action@v1

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: extraChIPs
-Version: 1.7.10
+Version: 1.8.1
 Title: Additional functions for working with ChIP-Seq data
 Authors@R: person("Stevie", "Pederson", 
   email = "[email protected]", 

R/importPeaks.R

@@ -95,7 +95,7 @@ importPeaks <- function(
     }
 
     ## Handle empty files separately first
-    if (file.size(x) == 0) return(GRanges(NULL, seqinfo = seqinfo))
+    if (.isEmpty(x)) return(GRanges(NULL, seqinfo = seqinfo))
 
     ## Define the parameters for the two types
     colNames <- c(
@@ -158,9 +158,10 @@ importPeaks <- function(
     }
 
     ## Handle empty files separately first
-    if (file.size(x) == 0) return(GRanges(NULL, seqinfo = seqinfo))
+    if (.isEmpty(x)) return(GRanges(NULL, seqinfo = seqinfo))
 
     ## Define the colnames
+    stopifnot(.isValidBed(x))
     nCol <- min(ncol(read.table(x, sep = "\t", nrows = 1)), 6)
     colNames <- c("seqnames", "start", "end", "name", "score", "strand")
     classes <- c(
@@ -245,3 +246,9 @@ importPeaks <- function(
     }
     all(allNumerics, strandOK)
 }
+
+.isEmpty <- function(x) {
+    ## This is a better approach then checking file.size, given that a
+    ## compressed empty file will have size ~20B
+    !length(readLines(x, n = 1))
+}

tests/testthat/test_importPeaks.R

@@ -80,9 +80,7 @@ test_that("seqinfo objects behave correctly for narrowPeak files", {
     )
   )
   ## Error
-  expect_error(
-    importPeaks(fl, "narrow", seqinfo = NULL)
-  )
+  expect_error(importPeaks(fl, "narrow", seqinfo = NULL))
   ## Error
   expect_error(
     importPeaks(fl, "narrow", glueNames = "{1:5}"), "length.+is not TRUE"
@@ -105,8 +103,8 @@ test_that("blacklists behave correctly",{
 
 
 test_that("Empty files parse empty GRanges", {
-  fl <- file.path(tempdir(), "empty.txt")
-  file.create(fl)
+  ## This now catches empty files that are compressed too!
+  fl <- system.file("extdata/empty.bed.gz", package = "extraChIPs")
   np1 <- importPeaks(fl, type = "narrow", setNames = FALSE)
   bp1 <- importPeaks(fl, type = "broad", setNames = FALSE)
   expect_true(is(c(np1, bp1), "GRangesList"))