Merge pull request #673 from sneumann/jomain

fix: fix for issue #511
sneumann · Apr 20, 2023 · 32ccff8 · 32ccff8
2 parents d09cbf3 + 2cf295a
commit 32ccff8
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Showing 4 changed files with 12 additions and 5 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -53,8 +53,8 @@ jobs:
       matrix:
         config:
           - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.17'}
-          - { os: windows-latest, r: 'devel', bioc: '3.17'}
+          - { os: macOS-latest, r: 'next', bioc: '3.17'}
+          - { os: windows-latest, r: 'next', bioc: '3.17'}
     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: 3.21.4
+Version: 3.21.5
 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/R/methods-XCMSnExp.R b/R/methods-XCMSnExp.R
@@ -2478,6 +2478,8 @@ setMethod(
             smpls <- factor(pks[, "sample"], levels = lvls)
             pks <- split.data.frame(pks, smpls)
             pkd <- split.data.frame(pkd, smpls)
+            mz <- matrix(mz, ncol = 2)
+            rt <- matrix(rt, ncol = 2)
         }
         res <- as(res, "XChromatograms")
         res@.Data <- matrix(
@@ -2492,8 +2494,8 @@ setMethod(
             ## Loop through each EIC "row" to ensure all features in
             ## that EIC are retained.
             fts <- lapply(seq_len(nrow(res)), function(r) {
-                fdev <- featureDefinitions(object, mz = mz(res)[r, ],
-                                           rt = rt)
+                fdev <- featureDefinitions(object, mz = mz[r, ],
+                                           rt = rt[r, ])
                 if (nrow(fdev)) {
                     fdev$row <- r
                     .subset_features_on_chrom_peaks(

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,8 @@
+Changes in version 3.21.5
+---------------------
+
+- Fix issue in `chromatogram` after filtering a result object (issue #511).
+
 Changes in version 3.21.4
 ---------------------