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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.