Erased the codesnippet from the vignette

R/createMassBank.R

@@ -1563,7 +1563,7 @@ addPeaks <- function(mb, filename_or_dataframe)
 	
 	cols <- c("cpdID", "scan", "mzFound", "int", "OK")
 	
-	n <- colnames(df
+	n <- colnames(df)
 	
 	# Check if comma-separated or semicolon-separated
 	d <- setdiff(cols, n)

vignettes/RMassBank.Rnw

@@ -282,29 +282,6 @@ First, create a workspace for the \Rvar{msmsWorkflow}:
 w <- newMsmsWorkspace()
 @
 
-
-
-Temporary deposit for the script using msmsRead. Build into actual vignette!
-<<eval=FALSE>>=
-
-#####SCRIPT
-library(RMassBank)
-loadRmbSettings("settings_comrecal_QEx_EX.INI")
-loadList("QEx_10_compoundlist.csv")
-msmsmzR <- newMsmsWorkspace()
-msmsXCMS <- newMsmsWorkspace()
-Args <- list(method="centWave", ppm = 5, snthresh = 1.5,
-    peakwidth = c(20,60), integrate = 1, mzdiff = -0.001, mzCenterFun = "meanApex3")
-msmsmzR <- msmsRead(msmsmzR, filetable = "Filelist_QEx.csv", readMethod="mzR", mode="pH", Args=Args)
-
-datadir <- "/vol/data_extern/emma.schymanski@ufz.de/Qexactive/10_centroided_mzMLs"
-files <- list.files(datadir, pattern=".mzML", full.names=TRUE)
-cpdid <- c(3035,2845,3040,3041,139,3046,297,3050,2856,3052)
-msmsXCMS <- msmsRead(msmsXCMS, files=files, cpdids = cpdid, readMethod="xcms",mode="pH",Args=Args)
-@
-
-
-
 The full paths of the files must be loaded into the container in the array
 \Rvar{files}: