fix: disable nested parallel processing for chromatograms

This fix addresses a comment in issue sneumann/xcms#627 (comment).
lgatto · Apr 30, 2024 · 72e4dab · 72e4dab
1 parent 6284cc6
commit 72e4dab
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MSnbase
 Title: Base Functions and Classes for Mass Spectrometry and Proteomics
-Version: 2.29.4
+Version: 2.29.5
 Description: MSnbase provides infrastructure for manipulation,
              processing and visualisation of mass spectrometry and
              proteomics data, ranging from raw to quantitative and

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # MSnbase 2.29
 
+## MSnbase 2.29.5
+
+- Disable nested parallel processing for `chromatogram()` method.
+
 ## MSnbase 2.29.4
 
 - Move XML to suggests.

diff --git a/R/functions-OnDiskMSnExp.R b/R/functions-OnDiskMSnExp.R
@@ -577,7 +577,7 @@ precursorValue_OnDiskMSnExp <- function(object, column) {
             match(fileNames(subs), fns),
             FUN = function(cur_sample, cur_file, rtm, mzm, aggFun) {
                 ## Load all spectra for that file. applies also any proc steps
-                sps <- spectra(cur_sample)
+                sps <- spectra(cur_sample, BPPARAM = SerialParam())
                 ## Related to issue #229: can we avoid getting all spectra and
                 ## just return the intensity values for each spectrum instead?
                 rts <- rtime(cur_sample)