Error when reading mzXML files (due to accent é è )

[yguitton]

Sometimes during MS files life they are stored under filepaths with accent (e.g in french metabolomics is métabolomique)
and so when converting to mzXML (or other format) sometimes those paths are kept in the file and we get error.

invalid UTF-8 input in readChar() ligne <parentFile fileName="file:///D:/JPA/Laits-2015-06-10-Exactive (Metabolomique R�cap)/./211114031_S5_.raw" for exemple

[lecorguille]

@sneumann You already help me with an issue with those kind of characters.
Your advice was to use LANG=C Rscript
In this case, it seems to not be enough.
Do you have an other tricks?
Many thanks

[sneumann]

Can you provide a small test file ? Yours, Steffen

[yguitton]

HI @sneumann , here enclosed two files the V1 generate the reported error and V2 not. The only difference is that i have manually removed the é in Metabolomique in V2 xml.
Thanks for your help

mzXML_files_forTest.zip

[sneumann]

Hi, sorry, can't reproduce here. I tried
export LOCALE="C" ; echo 'library(xcms);xcmsRaw("211114031S3V1.mzXML") ; sessionInfo()' | R --vanilla and it just worked. What is your locale as reported by sessionInfo() ?

[lecorguille]

Seems fix since: d649c25
@yguitton I have just tested your files in the prod instance and it works.