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

[Thomas Lawson]

Thanks Rainer!

Seems to be building and passing now :)
http://bioconductor.org/checkResults/devel/bioc-LATEST/msPurity/

Very strange that the error occurs so randomly - I will keep an eye out for
it.

Thanks,
Tom



On Mon, Apr 29, 2019 at 5:03 AM Rainer Johannes <Johannes.Rainer using eurac.edu>
wrote:

> 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
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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