[Bioc-devel] RMassBank build error
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Mon Oct 10 02:07:38 CEST 2016
You (and everyone else) should not construct new instances by using new()
together with prototype. It is true that we did that long time ago in
Biobase, but I think the collective lesson is that it is not really
flexible/stable enough (ok, bad wording, but it is Sunday night). What we
recommend now is to create a constructor function, usually the class name,
like GRanges(). Of course, inside the constructor you would then call
new(), which works ok for simple cases.
On Sun, Oct 9, 2016 at 4:02 PM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
>
> Dear Michael and RMassBank developers,
>
> On 9 October 2016 15:53, Stravs, Michael wrote:
>
> > 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
>
> I don't think that your initialize method will work as it is, because it
> passess arguments to callNextMethod, which doesn't have them. But, to be
> honest, I don't think that any intialize method will sort the current
> problem.
>
> I am not sure how to best handle to problem. To sort your problem, we
> (the MSnbase maintainers) could revert to our old initialize,Spectrum
> method, but some very weird bugs (in R? in some very low-level C code?)
> result in random crashes. We are looking for something else.
>
> Anyway, if we don't manage to find an acceptable solution for MSnbase, I
> will submit an RMassBank patch that will sort the error (and other
> things resulting from MSnbase improvements) out. What would be the best
> way to submit a patch - email, a pull request to a github repo?
>
> Best wishes,
>
> Laurent
>
> > 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/
> >>
>
>
> --
> Laurent Gatto | @lgatt0
> http://cpu.sysbiol.cam.ac.uk/
> http://lgatto.github.io/
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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