[Bioc-devel] S4 Method Slow Execution if Signature Has Multiple Class Unions

Hi Dario,

Thanks for bringing this up. The second time speed could be explained
by the caching that happens inside the methods package. If you are
able to come up with a smaller reproducible example, I would be happy
to help out.

Michael

On Mon, Nov 22, 2021 at 1:00 PM Dario Strbenac via Bioc-devel

Good day,

I created two constructor methods for a generic function. One is for the default empty constructor and the other is a constructor when any one or more parameters is specified by the user. The method signatures are:

1. c("missing", "missing", "missing", "missing", "missing", "missing", "missing", "missing"),
2. c("characterOrMissing", "numericOrMissing", "numericOrMissing", "numericOrMissing", "numericOrMissing", "characterOrMissing", "BiocParallelParamOrMissing", "numericOrMissing")

The class unions are defined as you might expect.

setClassUnion("characterOrMissing", c("character", "missing"))
setClassUnion("numericOrMissing", c("numeric", "missing"))
setClassUnion("BiocParallelParamOrMissing", c("BiocParallelParam", "missing"))

The first method works as expected:

system.time(CrossValParams())

   user  system elapsed
  0.165   0.000   0.165

The second takes over ten minutes and constantly uses 100% CPU usage, according to top.

system.time(CrossValParams("Leave-k-Out", leave = 2))

   user  system elapsed
760.018  15.093 775.090

Strangely, if I rerun this code again, it works quickly the second time.

system.time(CrossValParams("Leave-k-Out", leave = 2))

   user  system elapsed
  0.145   0.000   0.145

I haven't been able to come up with a minimal reproducile example of the issue. How can this be done consistently and efficiently?

--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

Hello,

Thanks. It was difficult to pinpoint, but I was able to make a minimal example. It happens only if SummarizedExperiment is pre-loaded. The difference is 0.2 seconds versus 32 seconds on my modest Windows 10 laptop computer - a 150 times slowdown. Can you reproduce it?

library(SummarizedExperiment)

setClassUnion("characterOrMissing", c("character", "missing"))
setClassUnion("integerOrMissing", c("integer", "missing"))
setClass("ParamsSet", representation(A = "characterOrMissing", B = "integer"))
setGeneric("ParamsSet", function(A, B, C, D, E, F, G, H) standardGeneric("ParamsSet"))

setMethod("ParamsSet", c("missing", "missing", "missing", "missing", "missing", "missing", "missing", "missing"),
function() # Empty constructor
{
  new("ParamsSet", A = 'M', B = 300L)
})

setMethod("ParamsSet", c("characterOrMissing", "integerOrMissing", "integerOrMissing", "integerOrMissing",
                         "characterOrMissing", "integerOrMissing", "integerOrMissing", "integerOrMissing"),
function(A = c('L', 'M', 'N'), B = 500, C = 100, D, E, F, G, H)
{
  if(missing(A)) A <- 'L' # Mimick match.arg.
  if(missing(B)) B <- 500L # Hack to implement parameter defaults not specified by generic.
  if(missing(C)) C <- 100L
  new("ParamsSet", A = A, B = B)
})

system.time(ParamsSet(B = 999L)) # Slow or fast, depending on SummarizedExperiment presence.

--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia