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

Thomas Lawson thom@@@n|ge|@|@w@on @end|ng |rom gm@||@com
Sun Apr 28 18:04:37 CEST 2019

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.

It might be due to this warning from XCMS (an xcmsSet object is used for

> 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,

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