[Bioc-devel] Mc OSX fail [MSData::Spectrum::getMZIntensityPairs()] Sizes do not match

Rainer Johannes Joh@nne@@R@|ner @end|ng |rom eur@c@edu
Mon Apr 29 06:03:13 CEST 2019

Hi Tom!

> On 28 Apr 2019, at 18:04, Thomas Lawson <thomas.nigel.lawson using gmail.com> wrote:
> Hi BioConductor community,
> My package (msPurity) is passing the build on the Linux and Windows servers
> but has just started failing on the Mac OS X server due to the following
> error when running the "purityX" constructor in the vignette :
>> Error: processing vignette 'msPurity-vignette.Rmd' failed with
> diagnostics: [MSData::Spectrum::getMZIntensityPairs()] Sizes do not match.

This error is occurring randomly on my mac too - it is originating from the proteowizard C++ code from within mzR. The problem is you can't do anything about it. This is a so far elusive error that I try to catch since more than a year. It occurs randomly, with some configurations (OS and compilers) less frequently, with others more. At present I get it more often if I read data from mzXML files, while mzML files seem to be OK-ish (???). 

Unfortunately I don't have a solution to this, sorry. It *should* go away in the next check build - hopefully.

cheers, jo

> It might be due to this warning from XCMS (an xcmsSet object is used for
> purityX)
>> Warning: Adjusted retention times had to be re-adjusted for some files to
> ensure them being in the same order than the raw retention times. A call to
> 'dropAdjustedRtime' might thus fail to restore retention times of
> chromatographic peaks to their original values. Eventually consider to
> increase the value of the 'span' parameter.
> And could be related to these issues
> - https://github.com/lgatto/MSnbase/issues/170
> - https://github.com/sneumann/mzR/issues/112
> However, I can't replicate the issue on my local OSX machine (or on local
> Linux and Windows machines) and it might be quite hard to troubleshoot.
> Interestingly though I was not experiencing this error since the weekend -
> and I have not updated the code for purityX for a while now - so perhaps an
> update in mzR or MSnBase might have occurred that has caused it?
> I have just pushed an update to BioCon dev where I have updated the
> vignette that might help stop the error (I removed the retention alignment
> step in XCMS prior to using purityX).
> Hopefully this will pass tonight, if it doesn't, is there anyway I could
> still get the package updates in the next release? Perhaps by having purityX
> as Linux and Windows only? (the main functionality is for the purityA
> class, so this wouldn't be a dramatic loss of functionality for the package)
> Kind regards,
> Tom
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