an update:
I've switched back to the "default" initialize methods for Spectrum1 and
Spectrum2 objects in MSnbase (not implemented in C) and with these installing
RMassBank seems to work.
I have however now to run some intense torture tests on MSnbase to ensure that
we don't run again into the random memory problems that we had in MSnbase
(issue https://github.com/lgatto/MSnbase/issues/138)
jo
> On 7 Oct 2016, at 20:14, Rainer Johannes <johannes.rai...@eurac.edu> wrote:
>
> we could try to switch back from the C-constructors to the "old" ones, I'll
> check later
>
>> On 7 Oct 2016, at 20:03, Schymanski, Emma <emma.schyman...@eawag.ch> wrote:
>>
>> Hi Laurent,
>>
>> I don't have an answer for you right now - but in CC are also the other 3
>> involved in trying to fix this on our side...
>> Just to make sure that all have the respective email addresses to try speed
>> up the debugging...
>>
>> Thanks!
>> Emma
>> ________________________________________
>> From: Laurent Gatto [lg...@cam.ac.uk]
>> Sent: Friday, 7 October 2016 7:52 PM
>> To: Schymanski, Emma; Martin Morgan
>> Cc: bioc-devel@r-project.org; Rainer Johannes
>> Subject: Re: [Bioc-devel] RMassBank build error
>>
>> 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/
>
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