From 718b36e546f1f4257fdc1a532a59eebfacf853f4 Mon Sep 17 00:00:00 2001
From: Chris Mitchell <chris@ginkgobioworks.com>
Date: Wed, 15 Nov 2017 12:48:59 -0500
Subject: [PATCH 1/2] Skip targets outside of scanrange

---
 R/xcmsRaw.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/R/xcmsRaw.R b/R/xcmsRaw.R
index 76ddb5f..5d8a32a 100644
--- a/R/xcmsRaw.R
+++ b/R/xcmsRaw.R
@@ -1172,6 +1172,14 @@ setMethod("findPeaks.centWave", "xcmsRaw", function(object, ppm=25, peakwidth=c(
       for (ti in 1:length(targets)) {
         target <- targets[[ti]]
         rtrange <- target$rtrange
+        if(rtrange[1] < scanrange[1]) {
+            cat("Warning: scanrange of ", rtrange[1], "less than minimum rtrange in file. Target ignored.\n")
+            next
+        }
+        if(rtrange[2] > scanrange[2]) {
+            cat("Warning: scanrange of ", rtrange[2], "greater than maximum rtrange in file. Target ignored.\n")
+            next
+        }
         mzrange <- target$mzrange
         t_peakwidth <- target$peakwidth
         if (is.null(t_peakwidth)) t_peakwidth <- peakwidth

From 9cb36f6018f08d92f7e7d9d8f40fee7661c30c59 Mon Sep 17 00:00:00 2001
From: Chris Mitchell <chris@ginkgobioworks.com>
Date: Wed, 15 Nov 2017 14:04:32 -0500
Subject: [PATCH 2/2] Check scmin and scmax instead of scan indices

---
 R/xcmsRaw.R | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/R/xcmsRaw.R b/R/xcmsRaw.R
index 5d8a32a..de08abb 100644
--- a/R/xcmsRaw.R
+++ b/R/xcmsRaw.R
@@ -1172,14 +1172,6 @@ setMethod("findPeaks.centWave", "xcmsRaw", function(object, ppm=25, peakwidth=c(
       for (ti in 1:length(targets)) {
         target <- targets[[ti]]
         rtrange <- target$rtrange
-        if(rtrange[1] < scanrange[1]) {
-            cat("Warning: scanrange of ", rtrange[1], "less than minimum rtrange in file. Target ignored.\n")
-            next
-        }
-        if(rtrange[2] > scanrange[2]) {
-            cat("Warning: scanrange of ", rtrange[2], "greater than maximum rtrange in file. Target ignored.\n")
-            next
-        }
         mzrange <- target$mzrange
         t_peakwidth <- target$peakwidth
         if (is.null(t_peakwidth)) t_peakwidth <- peakwidth
@@ -1195,6 +1187,11 @@ setMethod("findPeaks.centWave", "xcmsRaw", function(object, ppm=25, peakwidth=c(
         scmin <- si[1]
         scmax <- si[length(si)]
 
+        if(is.na(scmin) || is.na(scmax)) {
+            cat("Warning: scanrange ", rtrange, "outside rtrange in file. Target ignored.\n")
+            next
+        }
+
         rawmz <- rawMZ(object, mzrange=mzrange, scanrange=c(scmin, scmax))
         gz <- which(rawmz > 0)
         if (length(gz) > 0) {