From hpages at fhcrc.org  Tue Jul  2 07:59:05 2013
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Mon, 01 Jul 2013 22:59:05 -0700
Subject: [Rd] cache most-recent dispatch
In-Reply-To: <51D25F62.6050102@fhcrc.org>
References: <51D255CC.1050300@fhcrc.org> <51D25F62.6050102@fhcrc.org>
Message-ID: <51D26C29.80605@fhcrc.org>

Hi Val,

[off list... I don't want to compromise your chances to start a
constructive discussion ;-)]

Thanks for reporting this. Just wanted to mention that the reason I
think the situation is worst when you use the paste() generic defined
in BiocGenerics than when you make paste() a generic with
setGeneric("paste") is because of the signature of the generic.
With the latter dispatch is on the 'sep' and 'collapse' args only
(which is surprising but that's another story), while
with the former it's on ...:

   > setGeneric("paste")
   [1] "paste"

   > paste
   standardGeneric for "paste" defined from package "base"

   function (..., sep = " ", collapse = NULL)
   standardGeneric("paste")
   <environment: 0x157a028>
   Methods may be defined for arguments: sep, collapse
   Use  showMethods("paste")  for currently available ones.

   ## Note that showMethods() is broken (it contradicts the above
   ## that indicates dispatch is on 'sep' and 'collapse').
   > showMethods("paste")
   Function: paste (package base)
   ...="ANY"

   > microbenchmark(fun0(lst), fun1(lst), times=10)
   Unit: milliseconds
         expr       min        lq    median        uq       max neval
    fun0(lst) 27.374228 27.508580 28.144858 28.895889 33.528221    10
    fun1(lst)  5.474173  5.739289  5.803471  6.050482  6.825982    10

   > removeGeneric("paste")
   [1] TRUE

   > setGeneric("paste", signature="...")  # this how it's defined in 
BiocGenerics
   Creating a new generic function for ?paste? in the global environment
   [1] "paste"

   > microbenchmark(fun0(lst), fun1(lst), times=10)
   Unit: milliseconds
         expr        min         lq     median         uq        max neval
    fun0(lst) 149.828201 153.192866 155.845508 157.916067 176.313906    10
    fun1(lst)   4.924387   5.088094   5.114532   5.200432   5.332386    10

Dispatch on ... seems to have a ridiculously high cost!

H.

On 07/01/2013 10:04 PM, Valerie Obenchain wrote:
> Hi,
>
> S4 method dispatch can be very slow. Would it be reasonable to cache the
> most
> recent dispatch, anticipating the next invocation will be on the same
> type? This
> would be very helpful in loops.
>
>    fun0 <- function(x)
>        sapply(x, paste, collapse="+")
>    fun1 <- function(x) {
>        paste <- selectMethod(paste, class(x[[1]]))
>        sapply(x, paste, collapse="+")
>    }
>    lst <- split(rep(LETTERS, 100), rep(1:1300, 2))
>
>    library(microbenchmark)
>    microbenchmark(fun0(lst), times=10)
>    ## Unit: milliseconds
>    ##       expr      min       lq   median      uq      max neval
>    ##  fun0(lst) 4.153287 4.180659 4.513539 5.19261 5.280481    10
>
>    setGeneric("paste")
>    microbenchmark(fun0(lst), fun1(lst), times=10)
>    ## >     microbenchmark(fun0(lst), fun1(lst), times=10)
>    ## Unit: milliseconds
>    ##       expr       min       lq    median        uq       max neval
>    ##  fun0(lst) 21.093180 21.27616 21.453174 21.833686 24.758791    10
>    ##  fun1(lst)  4.517808  4.53067  4.582641  4.682235  5.121856    10
>
> Dispatch seems to be especially slow when packages are involved, e.g.,
> with the Bioconductor IRanges package
> (http://bioconductor.org/packages/release/bioc/html/IRanges.html)
>
>    removeGeneric("paste")
>    library(IRanges)
>    showMethods(paste)
>    ## Function: paste (package BiocGenerics)
>    ## ...="ANY"
>    ## ...="Rle"
>    selectMethod(paste, "ANY")
>    ## Method Definition (Class "derivedDefaultMethod"):
>    ##
>    ## function (..., sep = " ", collapse = NULL)
>    ## .Internal(paste(list(...), sep, collapse))
>    ## <environment: namespace:base>
>    ##
>    ## Signatures:
>    ##         ...
>    ## target  "ANY"
>    ## defined "ANY"
>
>    microbenchmark(fun0(lst), fun1(lst), times=10)
>    ## Unit: milliseconds
>    ##       expr        min         lq     median         uq        max
> neval
>    ##  fun0(lst) 233.539585 234.592491 236.311209 237.268506 243.181123
>     10
>    ##  fun1(lst)   4.564914   4.592996   4.642898   4.729009   5.492706
>     10
>
>    sessionInfo()
>    ## R version 3.0.0 Patched (2013-04-04 r62492)
>    ## Platform: x86_64-unknown-linux-gnu (64-bit)
>    ##
>    ## locale:
>    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>    ##  [7] LC_PAPER=C                 LC_NAME=C
>    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>    ##
>    ## attached base packages:
>    ## [1] parallel  stats     graphics  grDevices utils     datasets
> methods
>    ## [8] base
>    ##
>    ## other attached packages:
>    ## [1] IRanges_1.19.15      BiocGenerics_0.7.2   microbenchmark_1.3-0
>    ##
>    ## loaded via a namespace (and not attached):
>    ## [1] stats4_3.0.0
>
>
> Thanks,
> Valerie
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] cache most-recent dispatch
=?windows-1252?Q?Herv=E9_Pag=E8s?=