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