[R] xmlEventParse returning trimmed content?

[Johannes Graumann]

Hello,

I wrote the function below and have the problem, that the "text" bit returns 
only a trimmed version (686 chars as far as I can see) of the content under 
the "fetchPeaks" condition.
Any hunches why that might be?

Thanks for pointer, Joh

xmlEventParse(fileName,
    list(
      startElement=function(name, attrs){
        if(name == "scan"){
          if(.GlobalEnv$ms2Scan == TRUE & .GlobalEnv$scanDone == TRUE){
            cat(.GlobalEnv$scanNum,"\n")
            MakeSpektrumEntry()
          }
          .GlobalEnv$scanDone <- FALSE
          .GlobalEnv$fetchPrecMz <- FALSE
          .GlobalEnv$fetchPeaks <- FALSE
          .GlobalEnv$ms2Scan <- FALSE
          if(attrs[["msLevel"]] == "2"){
            .GlobalEnv$ms2Scan <- TRUE
            .GlobalEnv$scanNum <- as.integer(attrs[["num"]])
          }
        } else if(name == "precursorMz" & .GlobalEnv$ms2Scan == TRUE){
          .GlobalEnv$fetchPrecMz <- TRUE
        } else if(name == "peaks" & .GlobalEnv$ms2Scan == TRUE){
          .GlobalEnv$fetchPeaks <- TRUE
        }
      },
      text=function(text){
        if(.GlobalEnv$fetchPrecMz == TRUE){
          .GlobalEnv$precursorMz <- as.numeric(text)
          .GlobalEnv$fetchPrecMz <- FALSE
        }
        if(.GlobalEnv$fetchPeaks == TRUE){
          .GlobalEnv$peaks <- text
          .GlobalEnv$fetchPeaks <- FALSE
          .GlobalEnv$scanDone <- TRUE
        }
      }
    )
  )

> sessionInfo() 
R version 2.9.0 beta (2009-04-03 r48277) 
x86_64-pc-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] caMassClass_1.6 MASS_7.2-46     digest_0.3.1    caTools_1.9    
 [5] bitops_1.0-4.1  rpart_3.1-43    nnet_7.2-46     e1071_1.5-19   
 [9] class_7.2-46    PROcess_1.19.1  Icens_1.15.2    survival_2.35-4
[13] RCurl_0.94-1    XML_2.3-0       rkward_0.5.0   

loaded via a namespace (and not attached):
[1] tools_2.9.0

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