Hi, just wanted to note this (mild) regression. I tried saveXML(traml) with different compression= and indent= settings, but the output remained in a single line for XML-2.8-1
Without writing to a file the string representation after saveXML() looks quite similar, with the exception of a \n which seems to be at the end in XML-2.6 output and at the beginning (just after the <?xml?>) in XML-2.8-1. Nothing major, most annoying is the indentatino stuff, but the \n issue might point to the difference ? The code for my tests is at the end of this mail. Yours, Steffen ################################################################### > saveXML(traml, file="bug.xml") <?xml version="1.0"?> <TraML xmlns="http://psi.hupo.org/ms/traml"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; version="0.9.4" xsi:schemaLocation="http://psi.hupo.org/ms/traml TraML0.9.4.xsd"> <cvList> <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.29.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> </cvList> </TraML>sneum...@paddy:~/tex/papers/2009tandemms/ > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu other attached packages: [1] XML_2.8-1 saveXML(traml) [1] "<?xml version=\"1.0\"?>\n\n<TraML xmlns=\"http://psi.hupo.org/ms/traml\"; xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"; version=\"0.9.4\" xsi:schemaLocation=\"http://psi.hupo.org/ms/traml TraML0.9.4.xsd\">\n <cvList>\n <cv id=\"MS\" fullName=\"Proteomics Standards Initiative Mass Spectrometry Ontology\" version=\"2.29.0\" URI=\"http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo\"/>\n </cvList>\n</TraML> " ################################################################### > saveXML(traml, file="bug.xml") <?xml version="1.0"?> <TraML xmlns="http://psi.hupo.org/ms/traml"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; version="0.9.4" xsi:schemaLocation="http://psi.hupo.org/ms/traml TraML0.9.4.xsd"> <cvList> <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.29.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> </cvList> </TraML> > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu other attached packages: [1] XML_2.6-0 saveXML(traml) [1] "<?xml version=\"1.0\"?>\n <TraML xmlns=\"http://psi.hupo.org/ms/traml\"; xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"; version=\"0.9.4\" xsi:schemaLocation=\"http://psi.hupo.org/ms/traml TraML0.9.4.xsd\">\n <cvList>\n <cv id=\"MS\" fullName=\"Proteomics Standards Initiative Mass Spectrometry Ontology\" version=\"2.29.0\" URI=\"http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo\"/>\n </cvList>\n</TraML>\n" ################################################################### library(XML) tramlVersion="0.9.4" schemaLocation="http://psi.hupo.org/ms/traml TraML0.9.4.xsd" ## ## TraML Root ## traml = xmlTree(tag="TraML", attrs=c( version=tramlVersion, "xsi:schemaLocation"=schemaLocation), namespaces = c( "http://psi.hupo.org/ms/traml";, xsi="http://www.w3.org/2001/XMLSchema-instance";) ) ## ## CV List ## traml$addNode("cvList", close = FALSE) traml$addNode("cv", attrs=c( id="MS", fullName="Proteomics Standards Initiative Mass Spectrometry Ontology", version="2.29.0", URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo";)) traml$closeTag() ## cvList saveXML(traml) sessionInfo() -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ______________________________________________ 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.
