From a553d8bb487482c86ef5108831406f8d17b82523 Mon Sep 17 00:00:00 2001
From: jorainer <johannes.rainer@gmail.com>
Date: Wed, 8 May 2024 14:37:11 +0200
Subject: [PATCH] fix: ensure dropFeatureDefinitions correctly drops filled
 peaks

---
 .github/workflows/check-bioc.yml | 6 +++---
 DESCRIPTION                      | 2 +-
 NEWS.md                          | 8 ++++++++
 R/XcmsExperiment.R               | 5 ++---
 4 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 6372778e9..3681b8159 100644
--- 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
index 516e14be3..f435def08 100644
--- 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
index 3b183a3c2..b8090dde3 100644
--- 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
index 1c86f0496..aff6d3acd 100644
--- 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)
         }