Re: [Rd] sapply improvements

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Wed, 04 Nov 2009 15:50:51 -0500

S4 generics can specify a valueClass. Perhaps that could be used in those cases.

On Wed, Nov 4, 2009 at 3:24 PM, Duncan Murdoch <murdoch_at_stats.uwo.ca> wrote:

> On 11/4/2009 12:15 PM, William Dunlap wrote:

>>>
>>> -----Original Message-----
>>> From: r-devel-bounces_at_r-project.org
>>> [mailto:r-devel-bounces_at_r-project.org] On Behalf Of Duncan Murdoch
>>> Sent: Wednesday, November 04, 2009 8:47 AM
>>> To: michael.m.spiegel_at_gmail.com
>>> Cc: R-bugs_at_r-project.org; r-devel_at_stat.math.ethz.ch
>>> Subject: Re: [Rd] error in install.packages() (PR#14042)
>>>
>>> On 11/4/2009 11:05 AM, michael.m.spiegel_at_gmail.com wrote:
>>> > Full_Name: Michael Spiegel
>>> > Version: 2.10
>>> > OS: Windows Vista
>>> > Submission from: (NULL) (76.104.24.156)
>>> > > > The following error is produced when attempting to call
>>> > > > install.packages.  Here
>>> > is the results of the traceback:
>>> > >> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
>>> > Error in f(res) : invalid subscript type 'list'
>>> >> traceback()
>>> > 7: f(res)
>>> > 6: available.packages(contriburl = contriburl, method = method)
>>> > 5: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
>>> > >        method = method, available = available, destdir = destdir, >
>>> >  dependencies = dependencies, ...)
>>> > 4: install.packages(pkgs = c("OpenMx"), repos = repos)
>>> > 3: eval.with.vis(expr, envir, enclos)
>>> > 2: eval.with.vis(ei, envir)
>>> > 1: source("http://openmx.psyc.virginia.edu/getOpenMx.R")
>>> > > I've tracked the error down to somewhere in available.packages
>>> > > defined in
>>> > src\library\utils\R\packages.R.  I am guessing that the error in
>>> > version 2.10
>>> > has something to do with the change: "available.packages() gains a
>>> > 'filters'
>>> > argument for specifying the filtering operations performed on the
>>> > packages found
>>> > in the repositories."
>>>
>>> I've found the error, and will fix and commit to R-devel and R-patched.
>>>
>>> For future reference:  the problem was that it assigned the result of
>>> sapply() to a subset of a vector.  Normally sapply() simplifies its result
>>> to a vector, but in this case the result was empty, so sapply() returned an
>>> empty list; assigning a list to a vector coerced the vector to a list, and
>>> then the "invalid subscript type 'list'" came soon after.
>>
>> I've run into this sort of problem a lot (0-long input to sapply
>> causes it to return list()).  A related problem is that when sapply's
>> FUN doesn't always return the type of value you expect for some
>> corner case then sapply won't do the expected simplication.  If
>> sapply had an argument that gave the expected form of FUN's output
>> then sapply could (a) die if some call to FUN didn't return something
>> of that form and (b) return a 0-long object of the correct form
>> if sapply's X has length zero so FUN is never called.  E.g.,
>>   sapply(2:0, function(i)(11:20)[i], FUN.VALUE=integer(1)) # die on
>> third iteration
>>   sapply(integer(0), function(i)i>0, FUN.VALUE=logical(1)) # return
>> logical(0)
>>
>> Another benefit of sapply knowing the type of FUN's return value is
>> that it wouldn't have to waste space creating a list of FUN's return
>> values but could stuff them directly into the final output structure.
>> A list of n scalar doubles is 4.5 times bigger than double(n) and the
>> factor is 9.0 for integers and logicals.
>
>
> What do you think of the behaviour of the sapply function below?  (I
> wouldn't put it into R as it is, I'd translate it to C code to avoid the
> lapply call; but I'd like to get the behaviour right before doing that.)
>
> This one checks that the length() and typeof() results are consistent. If
> the FUN.VALUE has names, those are used (but it doesn't require the names
> from FUN to match).
>
> Duncan Murdoch
>
> sapply <- function(X, FUN, ..., simplify = TRUE, USE.NAMES = TRUE,
> FUN.VALUE)
> {
>    FUN <- match.fun(FUN)
>    answer <- lapply(X, FUN, ...)
>    if(USE.NAMES && is.character(X) && is.null(names(answer)))
>                names(answer) <- X
>    if(simplify) {
>        if (missing(FUN.VALUE)) {
>            if ((!length(answer))
>                || length(common.len <- unique(unlist(lapply(answer,
> length)))) != 1L)
>                return(answer)
>            common.names <- names(answer[[1L]])
>        } else {
>            common.len <- length(FUN.VALUE)
>            common.type <- typeof(FUN.VALUE)
>            common.names <- names(FUN.VALUE)
>            if (length(answer)) {
>                if (any( unlist(lapply(answer, length)) != common.len ))
>                    stop(sprintf("%s values must be of length %d", "FUN",
> common.len))
>                if (any( unlist(lapply(answer, typeof)) != common.type ))
>                    stop(sprintf("%s values must be of type '%s'", "FUN",
> common.type))
>                if (is.null(common.names))
>                    common.names <- names(answer[[1L]])
>            } else if (length(FUN.VALUE) > 1)
>                return(array(FUN.VALUE[0], dim=c(common.len, 0),
>                             dimnames= if(!is.null(common.names))
>                                       list(common.names,character(0))))
>            else
>                return(FUN.VALUE[0])
>        }
>        if(common.len == 1L)
>            unlist(answer, recursive = FALSE)
>        else if(common.len > 1L)
>            array(unlist(answer, recursive = FALSE),
>                  dim= c(common.len, length(X)),
>                  dimnames= if(!(is.null(common.names) &
>                                 is.null(n2 <- names(answer))))
> list(common.names,n2))
>        else answer
>    } else answer
> }
>
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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Wed 04 Nov 2009 - 21:00:54 GMT

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