[Bioc-devel] RMassBank build error
Stravs, Michael
Michael.Stravs at eawag.ch
Sun Oct 9 16:53:49 CEST 2016
Hi all,
I now have all packages installed to test things and can reproduce the
problem. I must confess that I don't have a deep understanding on how S4
initialization works, so solution attempts on my side are very
trial-and-errory.
I will have to look into the workings of these initialization methods
anyway in the future. The RMassBank version currently on Bioc-devel uses
the default constructor (i.e. doesn't actually define an "initialize"
method).
However, one of my development versions has an initialize method, which
I introduced to work around a bug with Versioned initialize (see my
question here [1], the reply [2], and my current code [3]). That one is
*also* incompatible with the new MSnbase constructors because of some
argument mapping issues (but there might also be a workaround for that.)
[1] https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008528.html
[2] https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008576.html
[3]
https://github.com/MassBank/RMassBank/blob/s4power/R/SpectrumMethods.R#L124
On 07.10.2016 22:34, Laurent Gatto wrote:
> On 7 October 2016 21:30, Rainer Johannes wrote:
>
>> 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)
> I have done the same thing, which also needed addressing some unit
> tests. I will push these updates to master for after a final package
> check, but wait for the results of your intense torture tests before
> committing to svn.
>
> Laurent
>
>> jo
>>
>>
>>> On 7 Oct 2016, at 20:14, Rainer Johannes <Johannes.Rainer at 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.Schymanski at 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 [lg390 at cam.ac.uk]
>>>> Sent: Friday, 7 October 2016 7:52 PM
>>>> To: Schymanski, Emma; Martin Morgan
>>>> Cc: bioc-devel at 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 at 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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