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

[Thomas Lawson]

Hi all,

The same error has occurred on the most recent build for OS X
http://bioconductor.org/checkResults/devel/bioc-LATEST/msPurity/celaya2-buildsrc.html
(
msPurity was passing the past few days and I haven't made any changes. As
Johannes mentioned - the error seems random and is from the proteowizard
C++ code from within mzR)

Hopefully it was pass again tonight (if the packages are scheduled to be
rebuild).

I was just wondering though, how this will effect the stable release of
msPurity?

Thanks,
Tom



On Tue, Apr 30, 2019 at 11:00 AM Thomas Lawson <
thomas.nigel.lawson using gmail.com> wrote:

> 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
>>
>>

	[[alternative HTML version deleted]]