fix: issue #654

- Fix problem with `fillChromPeaks` after `MatchedFilterParam` peak detection on
  very sparse data (i.e. data with many empty spectra).

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 3.21.0
+Version: 3.21.1
 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,

R/functions-XCMSnExp.R

@@ -438,10 +438,19 @@ dropGenericProcessHistory <- function(x, fun) {
         object, rt = range(peakArea[, c("rtmin", "rtmax")]) + c(-2, 2))
     object <- filterMsLevel(object, msLevel)
     if (!length(object)) {
-        message("FAIL: no MS level ", msLevel, " data available.")
+        message("FAIL: no data available for the requested m/z - rt range.")
         return(res)
     }
     spctr <- spectra(object, BPPARAM = SerialParam())
+    ## Issue #653: empty spectra is not supported; this is the same fix applied
+    ## to matchedFilter peak detection.
+    spctr <- lapply(spctr, function(z) {
+        if (!length(z@mz)) {
+            z@mz <- 0.0
+            z@intensity <- 0.0
+        }
+        z
+    })
     mzs <- lapply(spctr, mz)
     vps <- lengths(mzs)
     ints <- unlist(lapply(spctr, intensity), use.names = FALSE)
@@ -475,7 +484,7 @@ dropGenericProcessHistory <- function(x, fun) {
     mass <- brks[-length(brks)] + bin_half ## midpoint for the breaks
     mass_range <- range(mass)
 
-    for (i in 1:nrow(res)) {
+    for (i in seq_len(nrow(res))) {
         rtr <- peakArea[i, c("rtmin", "rtmax")]
         mzr <- peakArea[i, c("mzmin", "mzmax")]
         ## Ensure that the rt region is within the rtrange of the data.

inst/NEWS

@@ -1,3 +1,10 @@
+Changes in version 3.21.1
+----------------------
+
+- Fix error with `fillChromPeaks` on sparse data (many empty spectra) and peak
+  detection performed with `MatchedFilterParam` (issue #653).
+
+
 Changes in version 3.19.2
 ----------------------