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.law...@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.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
