Dear Emma, The error is very strange indeed, and I hope Martin can help us out here.
With the latest RMassBank and MSnbase, I get > new("RmbSpectrum2") Error in initialize(value, ...) : 'initialize' method returned an object of class “Spectrum2” instead of the required class “RmbSpectrum2” which reproduces the error. The RmbSpectrum2 class is defined in a standard way .RmbSpectrum2 <- setClass("RmbSpectrum2", representation = representation( satellite="logical", low="logical", rawOK ="logical", good = "logical", mzCalc = "numeric", formula = "character", dbe = "numeric", formulaCount = "integer", dppm = "numeric", dppmBest = "numeric", ok = "logical", info = "list" ), contains=c("Spectrum2"), prototype = prototype( satellite = logical(), low = logical(), rawOK = logical(), good = logical(), mzCalc = numeric(), formula = character(), dbe = numeric(), formulaCount = integer(), dppm = numeric(), dppmBest = numeric(), ok = logical(), info = list(), new("Versioned", versions=c(classVersion("Spectrum2"), RmbSpectrum2 = "0.1.0")) )) and > new("Spectrum2") Object of class "Spectrum2" Precursor: NA Retention time: : Charge: NA MSn level: 2 Peaks count: 0 Total ion count: 0 works. The MSnbase maintainers have had a bit of a struggle with spurious and stange failures in the recent past (see [1]). This ans a whole new backend in the package have led to the following initialize method, that constructs the class directly in C setMethod("initialize", "Spectrum2", function(.Object, msLevel = 2L, peaksCount = length(mz), rt = numeric(), acquisitionNum = NA_integer_, scanIndex = integer(), tic = 0L, mz = numeric(), intensity = numeric(), fromFile = numeric(), centroided = NA, smoothed = NA, polarity = NA_integer_, merged = 1, precScanNum = NA_integer_, precursorMz = NA, precursorIntensity = NA, precursorCharge = NA_integer_, collisionEnergy = NA) { .Object <- Spectrum2_mz_sorted(msLevel, peaksCount, rt, acquisitionNum, scanIndex, tic, mz, intensity, fromFile, centroided, smoothed, polarity, merged, precScanNum, precursorMz, precursorIntensity, precursorCharge, collisionEnergy) if (validObject(.Object)) .Object }) Why is calling new("RmbSpectrum2") direclty returning an Spectrum2 object? Is this due to us not calling callNextMethod? Laurent [1] https://github.com/lgatto/MSnbase/issues/138 On 7 October 2016 17:02, Schymanski, Emma wrote: > Hi BioC team, > > In all the mzR troubles, it slipped through that RMassBank had a build error > of it's own presumably caused by an update to MSnbase - for some reason we > never received the email with the build error reports?! > We have discovered the error now, very late, and are onto finding out the > cause to fix it but it is not straightforward. Now that it is the day of the > deadline to pass build without error, are we able to have a little leeway if > needed? It's taken us the whole day to get the right binaries to actually > have a chance to start fixing... > Can someone also check or explain why we no longer receive the emails > reporting errors to us? > > Thanks, > Emma (on behalf of the others) > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel