From hpages at fhcrc.org  Fri May 30 21:53:57 2014
From: hpages at fhcrc.org (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Fri, 30 May 2014 12:53:57 -0700
Subject: [Rd] Style question
In-Reply-To: <CADwqtCO1GRU+k6G+iYTzx1khZWKZTL0uxDwbezKX-ReHoi+DFA@mail.gmail.com>
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Message-ID: <5388E1D5.7030902@fhcrc.org>

Hi Gabe,

On 05/30/2014 11:34 AM, Gabriel Becker wrote:
> This isn't likely to make much difference in most cases, but calling a
> function via :: can incur up to about twice the overhead on average
> compared to calling an imported function
>
>  > fun1
> function ()
> file_ext("text.txt")
> <environment: namespace:imptest>
>  > fun2
> function ()
> tools::file_ext("text.txt")
> <environment: namespace:imptest>
>  > microbenchmark(fun1(), times=10000)
> Unit: microseconds
>     expr    min     lq median      uq     max neval
>   fun1() 24.506 25.654 26.324 27.8795 154.001 10000
>  > microbenchmark(fun2(), times=10000)
> Unit: microseconds
>     expr    min      lq  median      uq     max neval
>   fun2() 42.723 46.6945 48.8685 52.0595 2021.91 10000

Interesting. Or with a void function so the timing more closely
reflects the time it takes to look up the symbol:

   > void
   function ()
   NULL
   <environment: namespace:S4Vectors>

   > fun1
   function ()
   void()
   <environment: namespace:IRanges>

   > fun2
   function ()
   S4Vectors::void()
   <environment: namespace:IRanges>

   > microbenchmark(fun1(), times=10000)
   Unit: nanoseconds
      expr min  lq median  uq   max neval
    fun1() 261 268    270 301 11960 10000
   > microbenchmark(fun2(), times=10000)
   Unit: microseconds
      expr    min     lq median     uq      max neval
    fun2() 13.486 14.918 15.782 16.753 60542.19 10000

S4Vectors::void() is about 60x slower than void()!

Cheers,
H.

>
> Also, if one uses roxygen2 (or even if one doesn't) ##'@importFrom above
> the function doing the calling documents this.
>
> And of course if you need to know where a function lives environment
> will tell you.
>
> ~G
>
>
> On Fri, May 30, 2014 at 10:00 AM, Hadley Wickham <h.wickham at gmail.com
> <mailto:h.wickham at gmail.com>> wrote:
>
>      > There is at least one subtle consequence to keep in mind when doing
>      > this. Of course, whatever choice you make, if the whatever() function
>      > moves to a different package, this breaks your package.
>      > However, if you explicitly import the function, your package will
>      > break at load-time (which is good) and you'll only have to modify
>      > 1 line in the NAMESPACE file to fix it. But if you do
>     foo::whatever(),
>      > your package won't break at load-time, only at run-time. Also you'll
>      > have to edit all the calls to foo::whatever() to fix the package.
>      >
>      > Probably not a big deal, but in an environment like Bioconductor
>     where
>      > infrastructure classes and functions can be shared by hundreds of
>      > packages, having people use foo::whatever() in a systematic way would
>      > probably make maintenance a little bit more painful than it needs to
>      > be when the need arises to reorganize/refactor parts of the
>      > infrastructure. Also, the ability to quickly grep the NAMESPACE
>      > files of all BioC packages to see who imports what is very convenient
>      > in this situation.
>
>     OTOH, I think there's a big benefit to being able to read package code
>     and instantly know where a function comes from.
>
>     Personally, I found this outweighs the benefits that you outline:
>
>     * functions rarely move between packages, and gsubbing for pkga:foo to
>     pkgb:foo isn't hard
>     * it's not that much hard to grep for pkg::foo in R/* than it is to
>     grep NAMESPACE
>
>     Hadley
>
>     --
>     http://had.co.nz/
>
>     ______________________________________________
>     R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
>     https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
>
> --
> Gabriel Becker
> Graduate Student
> Statistics Department
> University of California, Davis

-- 
Herv? Pag?s

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[Rd] Style question
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