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>sneumann at 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