[Rd] inspect [Was: R-devel Digest, Vol 83, Issue 2]

From: Simon Urbanek <simon.urbanek_at_r-project.org>
Date: Sat, 02 Jan 2010 19:49:46 -0500

On Jan 2, 2010, at 5:41 PM, Romain Francois wrote:

> On 01/02/2010 11:12 PM, Duncan Murdoch wrote:

>> 
>> On 02/01/2010 3:16 PM, Laurent Gautier wrote:
>>> On 1/2/10 8:53 PM, Duncan Murdoch wrote:
>>>> Simon Urbanek wrote:
>>>>> On Jan 2, 2010, at 12:17 PM, Laurent Gautier wrote:
>>>>> 
>>>>>> On 1/2/10 5:56 PM, Duncan Murdoch wrote:
>>>>>>> On 02/01/2010 11:36 AM, Laurent Gautier wrote:
>>>>>>>> [Disclaimer: what is below reflects my understanding from reading
>>>>>>>> the
>>>>>>>> R source, others will correct where deemed necessary]
>>>>>>>> 
>>>>>>>> On 1/2/10 12:00 PM, r-devel-request_at_r-project.org wrote:
>>>>>> (...)
>>>>>> 
>>>>>>>>> I'd also be interested if there is some ideas on the relative
>>>>>>>>> efficiency
>>>>>>>>> of the preserve/release mechanism compared to PROTECT/UNPROTECT.
>>>>>>>> PROTECT/UNPROTECT is trading granularity for speed. It is a stack
>>>>>>>> with
>>>>>>>> only tow operations possible:
>>>>>>>> - push 1 object into the stack
>>>>>>>> - pull (unprotect) N last objects from the stack
>>>>>>> UNPROTECT_PTR is also possible, which does a linear search through
>>>>>>> the
>>>>>>> stack and unprotects something possibly deep within it. There is also
>>>>>>> REPROTECT which allows you to replace an entry within the stack.
>>>>>>> 
>>>>>>> I would guess that UNPROTECT_PTR is more efficient than
>>>>>>> RecursiveRelease
>>>>>>> because it doesn't use so much stack space when it needs to go deep
>>>>>>> into
>>>>>>> the stack to release, but it is possible the compiler recognizes the
>>>>>>> tail recursion and RecursiveRelease is implemented efficiently. In
>>>>>>> that
>>>>>>> case it could be more efficient than UNPROTECT_PTR, which has to move
>>>>>>> all the other entries down to fill the newly vacated space. Really
>>>>>>> the
>>>>>>> only reliable way to answer efficiency questions like this is to try
>>>>>>> both ways and see which works better in your application.
>>>>>> Thanks. I did not know about UNPROTECT_PTR.
>>>>>> I had concerns over the stack usage, but so far it did not prove too
>>>>>> much of a problem. Still, why isn't the tail recursion explicitly
>>>>>> made an iteration then ? This would take the "may be the compiler
>>>>>> figures it out, may be not" variable out of the equation.
>>>>>> 
>>>>> Careful - the protection stack (bookkeeping by R) has nothing to do
>>>>> with the C function call stack hence it has nothing to do with the
>>>>> compiler. The protection stack is global so usually you don't run out
>>>>> of it unless something goes horribly wrong (=infinite loop).
>>>> I think Laurent was referring to RecursiveRelease, which could use a lot
>>>> of C stack if you choose to release something that is deep in the list,
>>>> since it checks the head, and if that doesn't match, calls itself again
>>>> on the rest of the list. (I checked, and at least one version of gcc
>>>> doesn't recognize the tail recursion: it really does generate a
>>>> recursive call.)
>>>> 
>>>> Laurent asked why it isn't optimized to avoid the recursion: I think the
>>>> answer is simply because it is so rarely used that nobody has bothered.
>>> 
>>> Yes, I was referring to RecursiveRelease. Sorry if this was not clear.
>>> 
>>> What are the chances for a patch to be accepted ? At first sight(*),
>>> making that tail recursion an iterative function is not a major
>>> undertaking, and reviewing the patch be fairly straightforward... but
>>> I can always use that time otherwise if the answer to the question is
>>> "nil".
>> 
>> I don't think I would want to review such a patch (I don't know the
>> memory manager well, I don't know that there is really a case where it
>> matters enough to be worth doing), so I'd say if you don't get a message
>> from a core member volunteering to do so, you should assume it won't be
>> accepted. But that doesn't mean you shouldn't write the code for your
>> own internal use and edification, and if you can put together a demo
>> that shows it really makes a big difference in a realistic situation,
>> you might get a different response.
>> 
>> Duncan Murdoch

>
> From what I understand, this has little to do with the memory manager, and resumes to the simple problem "how to remove an object from a list".
>
> Something like this, using the amazing inline and inspect packages:
>
> require( inline )
> require( inspect )
>

FWIW inspect is now part of R itself but as an internal function so you can either use it directly via .Internal or for compatibility inspect <- function(...) .Internal(inspect(...)) the arguments are (x, max.depth=-1, max.elements=5) [the last one is only supported in R-devel].

Cheers,
Simon

> remover <- cfunction(signature( list = "language", object = "environment" ), '
> if( !isNull( list ) ){
> SEXP x = list ;
> SEXP y ;
> while( CAR(x) != object && CADR(x) != R_NilValue ){
> y = x ;
> x = CDR(x) ;
> }
> if( CAR(x) == object ) SETCDR(y, CDR(x) ) ;
> }
> return list ;
> ', Rcpp=FALSE, verbose=FALSE )
>
> e <- new.env()
> call <- call( "foo", e, e, 1:10, 3 )
> call
> # inspect( call )
> result <- remover( call ,e )
> result
> # inspect( result )
>
> gives this :
>
> foo(10, <environment>, 0, <environment>, 1)
> @0x9f4e0d0 06 LANGSXP [NAM(2)]
> @0x9f4e204 01 SYMSXP [] "foo"
> @0xa907b78 14 REALSXP [NAM(2)] (len=1, tl=1763713056)
> @0x9f4d564 04 ENVSXP [NAM(1)]
> FRAME:
> @0x9e94a10 00 NILSXP [MARK,NAM(2)]
> ENCLOS:
> @0x9eb7b4c 04 ENVSXP [MARK,NAM(2),GP(0x8000)]
> HASHTAB:
> @0x9e94a10 00 NILSXP [MARK,NAM(2)]
> @0xa907b58 14 REALSXP [NAM(2)] (len=1, tl=1936941344)
> @0x9f4d564 04 ENVSXP [NAM(1)]
> FRAME:
> @0x9e94a10 00 NILSXP [MARK,NAM(2)]
> ENCLOS:
> @0x9eb7b4c 04 ENVSXP [MARK,NAM(2),GP(0x8000)]
> HASHTAB:
> @0x9e94a10 00 NILSXP [MARK,NAM(2)]
> @0xa907b38 14 REALSXP [NAM(2)] (len=1, tl=543908709)
> NULL
> ==================
> foo(10, 0, <environment>, 1)
> @0x9f4e0d0 06 LANGSXP [NAM(2)]
> @0x9f4e204 01 SYMSXP [] "foo"
> @0xa907b78 14 REALSXP [NAM(2)] (len=1, tl=1763713056)
> @0xa907b58 14 REALSXP [NAM(2)] (len=1, tl=1936941344)
> @0x9f4d564 04 ENVSXP [NAM(2)]
> FRAME:
> @0x9e94a10 00 NILSXP [MARK,NAM(2)]
> ENCLOS:
> @0x9eb7b4c 04 ENVSXP [MARK,NAM(2),GP(0x8000)]
> HASHTAB:
> @0x9e94a10 00 NILSXP [MARK,NAM(2)]
> @0xa907b38 14 REALSXP [NAM(2)] (len=1, tl=543908709)
> NULL
>
>
>
> so it boils down to this as a replacement to RecursiveRelease :
>
> /**
> * Removes the first instance of object with the list
> */
> static SEXP RemoveFromList( SEXP object, SEXP list){
> if( !isNull( list ) ){
> SEXP x = list ;
> SEXP y ;
> while( CAR(x) != object && CADR(x) != R_NilValue ){
> y = x ;
> x = CDR(x) ;
> }
> if( CAR(x) == object ) SETCDR(y, CDR(x) ) ;
> }
> return list ;
> }
>
>
> Romain
>
>
> --
> Romain Francois
> Professional R Enthusiast
> +33(0) 6 28 91 30 30
> http://romainfrancois.blog.free.fr
> |- http://tr.im/IW9B : C++ exceptions at the R level
> |- http://tr.im/IlMh : CPP package: exposing C++ objects
> `- http://tr.im/HlX9 : new package : bibtex
>
>
>
>



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