Error in Step 6. Aggregate recalibrated results: cleanElnoise() with new RMB

[sneumann]

Hi,
when using an up-to-date RMB we get the error:

msmsWorkflow: Step 6. Aggregate recalibrated results
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘cleanElnoise’ for signature ‘"RmbSpectraSet", "NULL", "numeric"’
Calls: runContributorToMassBankWorkflow ... lapply -> lapply -> lapply -> lapply -> FUN -> <Anonymous>

Yours,
Steffen

[sneumann]

This is a duplicate of MassBank/RMassBank#239
Yours, Steffen

[sneumann]

The stack trace is

9: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
       sQuote(fdef@generic), sQuote(cnames)), domain = NA)
8: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, 
               ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("RmbSpectraSet", "NULL", "numeric"), new("standardGeneric", 
       .Data = function (peaks, noise = getOption("RMassBank")$electronicNoise, 
           width = getOption("RMassBank")$electronicNoiseWidth) 
       standardGeneric("cleanElnoise"), generic = "cleanElnoise", 
       package = "RMassBank", group = list(), valueClass = character(0), 
       signature = c("peaks", "noise", "width"), default = NULL, 
       skeleton = (function (peaks, noise = getOption("RMassBank")$electronicNoise, 
           width = getOption("RMassBank")$electronicNoiseWidth) 
       stop("invalid call in method dispatch to 'cleanElnoise' (no default method)", 
           domain = NA))(peaks, noise, width)), <environment>)
7: FUN(X[[i]], ...)
6: lapply(as.list(X), match.fun(FUN), ...)
5: lapply(as.list(X), match.fun(FUN), ...)
4: lapply(w@spectra, cleanElnoise, noise = settings$electronicNoise, 
       width = settings$electronicNoiseWidth)
3: lapply(w@spectra, cleanElnoise, noise = settings$electronicNoise, 
       width = settings$electronicNoiseWidth)
2: msmsWorkflow(w = msmsList, mode = ionMode, steps = c(2, 3, 6, 
       7, 8), archivename = runId, newRecalibration = FALSE)
1: runContributorToMassBankWorkflow(folder, applyIntensityThreshold, 
       reprocess = FALSE)

and this is coming from this line of code:

RMassBank_mFam/galaxy/msp2massbank.r

Line 2199 in 6409efe

msmsList <- msmsWorkflow(w = msmsList, mode = ionMode, steps = c(2,3,6,7,8), archivename = runId, newRecalibration = FALSE)

Yours, Steffen

[sneumann]

Hi,
Judging from the error message signature ‘"RmbSpectraSet", "NULL", "numeric"’
and that the error comes from:
https://github.com/MassBank/RMassBank/blob/f23bce80beb20d4a6dfc30d851e467175256c8c7/R/leMsMs.r#L262
I guess there is no noise defined in the (generated) file:
/tmp/msp2massbank/RMassBank/Part_1_1__1_files__2_cpds/Settings_1_1__1_files__2_cpds.ini
and indeed there I see:

...
electronicNoise: 
electronicNoiseWidth: 0.3
...