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sneumann / mzR-playground

Playground area for the mzR package. The main code repository is now at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR/
http://bioconductor.org/packages/devel/bioc/html/mzR.html
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openMSfile takes ages for mzML #13

Closed sneumann closed 13 years ago

sneumann commented 13 years ago

Hi,

with an example file from Stephan Beisken openMSfile("20101004_1-Kestose.mzML") takes ~20 minutes.

Could be either in pwiz or RAMPadapter doing something inefficient.

Yours, Steffen

lgatto commented 13 years ago

That's very surprising indeed. Do you have the file? What's its size? How was it generated? Has he tested other similar files?

Laurent

sneumann commented 13 years ago

Issue solved, says Matt Chambers:

On Wed, 2011-07-20 at 12:19 -0500, Matthew Chambers wrote: OK, the index attribute is the culprit. When the spectrum::index doesn't match the index that we

calculate when creating our index from an unindexed mzML, it will recreate the index. This happens on every spectrum because the index is wrong in the file (always set to 1). I will take care of this in the next couple weeks (I want to merge the index maintenance between the chromatogram list and the spectrum list and that will take some work). They definitely need to fix their mzML exporter!