Hi.
I'm maintaining a package that creates an object that is essentially a
classed version of numeric. I updated recently from 2.7.1 to 2.9.0,
and merges involving my class suddenly took a huge performance hit.
I've traced the problem to something near rank(). From NEWS, it seems
rank() etc. changed in 2.8.0. Methods for xtfrm() are supposed to
help, but I've had no success. There was some chatter about this in
the archives back in Sept 08 (though apparently regarding S4), with a
suggestion that it is related to `[.` methods. That has been my
experience. In the toy example below, the problem disappears if
`[.my` is not defined. Under R 2.7.1 on Mac, both cat() statements
take the same amount of time, and that time depends very little on the
length of x. Under 2.9.0, the classed version takes much longer, and
the time grows (more than?) exponentially with length(x).
Is there something I can do to xtfrm.my() or [.my(), etc. to restore
the performance?
Thanks in advance,
Tim.
rm(list=ls())
as.my <- function(x,...)UseMethod('as.my')
as.my.default <- function(x,...)structure(x, class=c('my',class(x)))
`[.my` <- function (x, ...) structure(NextMethod("["), class =
class(x))
xtfrm.my <- function(x)as.numeric(x)
x <- 1:10000
cat(system.time(rank(x))[3]);cat(' ')
cat(system.time(rank(as.my(x)))[3]);cat('\n')
On Sat, May 30, 2009 at 10:58 AM, Tim Bergsma <timb at metrumrg.com> wrote:> Hi. > > I'm maintaining a package that creates an object that is essentially a > classed version of numeric. ?I updated recently from 2.7.1 to 2.9.0, > and merges involving my class suddenly took a huge performance hit. > I've traced the problem to something near rank(). ?From NEWS, it seems > rank() etc. changed in 2.8.0. ?Methods for xtfrm() are supposed to > help, but I've had no success. ?There was some chatter about this in > the archives back in Sept 08 (though apparently regarding S4), with a > suggestion that it is related to `[.` methods. ?That has been my > experience. ?In the toy example below, the problem disappears if > `[.my` is not defined. ?Under R 2.7.1 on Mac, both cat() statements > take the same amount of time, and that time depends very little on the > length of x. ?Under 2.9.0, the classed version takes much longer, and > the time grows (more than?) exponentially with length(x). > > Is there something I can do to xtfrm.my() or [.my(), etc. to restore > the performance? > > Thanks in advance, > > Tim. > > rm(...deleted rest of line...OUCH!!! Please don't post code like that. Someone may wipe out valuable objects in their workspace.
Tim Bergsma wrote:> Hi. > > I'm maintaining a package that creates an object that is essentially a > classed version of numeric. I updated recently from 2.7.1 to 2.9.0, > and merges involving my class suddenly took a huge performance hit. > I've traced the problem to something near rank(). From NEWS, it seems > rank() etc. changed in 2.8.0. Methods for xtfrm() are supposed to > help, but I've had no success. There was some chatter about this in > the archives back in Sept 08 (though apparently regarding S4), with a > suggestion that it is related to `[.` methods. That has been my > experience. In the toy example below, the problem disappears if > `[.my` is not defined. Under R 2.7.1 on Mac, both cat() statements > take the same amount of time, and that time depends very little on the > length of x. Under 2.9.0, the classed version takes much longer, and > the time grows (more than?) exponentially with length(x). > > Is there something I can do to xtfrm.my() or [.my(), etc. to restore > the performance? >If the object x you pass to xtfrm evaluates is.object(x) as false, you'll get fast behaviour, because it will use internal methods. If you have a class on it, you'll get dispatch to your method for every comparison, which will be slow. So if speed matters, I would not define an xtfrm.my, I would unclass things before sorting. Prior to a day or so ago, the dispatch for comparison methods was broken, and you would get a mix of internal and external comparisons. I suspect fixing that bug has made it even slower if you choose to try to sort a classed object. Duncan Murdoch> Thanks in advance, > > Tim. > > rm(list=ls()) > as.my <- function(x,...)UseMethod('as.my') > as.my.default <- function(x,...)structure(x, class=c('my',class(x))) > `[.my` <- function (x, ...) structure(NextMethod("["), class = class(x)) > xtfrm.my <- function(x)as.numeric(x) > x <- 1:10000 > cat(system.time(rank(x))[3]);cat(' ') > cat(system.time(rank(as.my(x)))[3]);cat('\n') > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >