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 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