Re: [Bioc-devel] RMassBank build error

[Martin Morgan]

On 10/07/2016 01:52 PM, Laurent Gatto wrote:

Dear Emma,

The error is very strange indeed, and I hope Martin can help us out here.

I did look at this a little but not completely, and it seems like you've 
come up with another solution? So I'll stop.

also for the intermittent error you mention, I skimmed the issue and saw 
the problem with the reference class finalizer. Roughly my understanding 
of what happens is

env = new.env()
env$f = function(...) message("done")
reg.finalizer(env, env$f)
rm(env); gc()

The garbage collector runs, marking env and other objects as available 
for re-use. Once the garbage collector is finished (not just collecting 
env, but all objects), any finalizers that are now eligible for 
evaluation are run. So there is a chance that the environment itself has 
been re-used by the time the finalizer runs, leading to intermittent errors.

This makes finalizers on reference classes unreliable.

Martin


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)
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