Merge remote-tracking branch 'Bioconductor/master'

# Conflicts:
#	DESCRIPTION
#	R/createMassBank.R
#	R/getSplash.R
#	R/leMsMs.r
#	R/leMsmsRaw.R

DESCRIPTION

 Package: RMassBank
 Type: Package
 Title: Workflow to process tandem MS files and build MassBank records
-Version: 2.3.1
+Version: 2.7.0
 Authors@R: c(
     person(given = "RMassBank at Eawag", email = "massbank@eawag.ch",
     role=c("cre")),

R/getSplash.R

@@ -62,8 +62,8 @@ filter_spectrum <- function(peaks, top_ions = NULL, base_peak_percentage = NULL)
         peaks <- peaks[peaks[,2] >= base_peak_percentage * base_peak_intensity, , drop=FALSE]
     }
 
-    ## Filter by top ions if specified
-    if (!missing(top_ions)) {
+    return(splash)
+}
         o <- order(-1*peaks[,2], peaks[,1], decreasing=FALSE)[seq(1:min(top_ions, nrow(peaks)))]
         peaks <- peaks[o, , drop=FALSE]
     }

R/leMsmsRaw.R

@@ -245,6 +245,14 @@ findMsMsHR.mass <- function(msRaw, mz, limit.coarse, limit.fine, rtLimits = NA,
 				childHeaders <- headerData[(headerData$precursorScanNum == masterScan) 
 								& (headerData$precursorMZ > mz - limit.coarse) 
 								& (headerData$precursorMZ < mz + limit.coarse) ,]
+				
+				# Fix 9.10.17: headers now include non-numeric columns, leading to errors in data conversion.
+				# Remove non-numeric columns
+				headerCols <- colnames(masterHeader)
+				headerCols <- headerCols[unlist(lapply(headerCols, function(col) is.numeric(masterHeader[,col])))]
+				masterHeader <- masterHeader[,headerCols,drop=FALSE]
+				childHeaders <- childHeaders[,headerCols,drop=FALSE]
+				
 				childScans <- childHeaders$seqNum
 				
 				msPeaks <- mzR::peaks(msRaw, masterHeader$seqNum)