Hi Tom! > On 28 Apr 2019, at 18:04, Thomas Lawson <thomas.nigel.law...@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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
