Merge pull request #745 from sneumann/fix_dropFeatureDefinitions

fix: ensure dropFeatureDefinitions correctly drops filled peaks
sneumann · May 13, 2024 · 386bd40 · 386bd40
2 parents c84c34c + a553d8b
commit 386bd40
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Showing 4 changed files with 14 additions and 7 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -53,9 +53,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'next', bioc: '3.19'}
-          - { os: windows-latest, r: 'next', bioc: '3.19'}
+          - { 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" }
+          - { 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 }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.2.0
+Version: 4.2.1
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# xcms 4.2
+
+## Changes in version 4.2.1
+
+- Fix in `dropFeatureDefinitions()` that was not correctly removing additional
+  metadata from gap-filled chromatographic peaks.
+
+
 # xcms 4.1
 
 ## Changes in version 4.1.13

diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
@@ -1553,9 +1553,8 @@ setMethod(
             object@processHistory, type = .PROCSTEP.PEAK.GROUPING, num = 1L)
         object@featureDefinitions <- .empty_feature_definitions()
         if (.hasFilledPeaks(object)) {
-            object@chromPeaks <- object@chromPeaks[
-                                            !object@chromPeakData$is_filled, ,
-                                            drop = FALSE]
+            object <- .filter_chrom_peaks(
+                object, which(!.chromPeakData(object)$is_filled))
             object@processHistory <- dropProcessHistoriesList(
                 object@processHistory, type = .PROCSTEP.PEAK.FILLING)
         }