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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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header() error #197

Closed magnuspalmblad closed 4 years ago

magnuspalmblad commented 5 years ago

I get the following error when trying to read the header info from an mzML file generated with msconvert (3.0.19120 and 3.0.11537) using the mzR header() function:

Error in object@backend$getAllScanHeaderInfo() : [read_file_header()] Unable to open file 2018-10-18_HeLa_OTOT.mzML (invalid permission or file locked)

The openMSfile(), instrumentInfo() and tic() functions work without error. I get the same error on any mzML file. Any ideas?

I run 64-bit R 3.5.2 under Windows 7.

lgatto commented 5 years ago

I don't know about the issue, unfortunately - I have never seen the invalid permission of file locked message. Is the data local, or do you access it over the network?

By the way, you should look in MSnbase and the readMSData(..., mode = "onDisk") function rather than using the raw mzR interface. Using the former will get you the fast on disk access from mzR with a well defined interface and support for multiple files. Note that this is unlikely to fix you issue, unfortunately, but will make you life easier.

magnuspalmblad commented 5 years ago

Thanks for the hint! Moving over to MSnbase now. Should give me more control, and hopefully help diagnose/find a workaround for these issues. The file is local, and seems to open fine with readMSData().