From @zwj|08 @end|ng |rom gm@||@com  Fri May 17 19:06:47 2019
From: @zwj|08 @end|ng |rom gm@||@com (=?UTF-8?B?5LuL6Z2e546L?=)
Date: Fri, 17 May 2019 09:06:47 -0800
Subject: [Rd] ALTREP: Bug reports
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Message-ID: <CAGiFhPPjGryNcsSr=7+9Z744RDobWfRQiGO0MgycZDf-nubC0g@mail.gmail.com>

Thank you very much for your answer. If I understand it correctly, for an
ALTREP class, a non-deep copy only creates a new ALTREP object but refers
to the same underlying SEXP as the old ALTREP object has, is it correct?
But since they all share the same underlying SEXP, will change of the value
in the old ALTREP object cause the change of the value in the new ALTREP
object? Or do you mean we need to decide which SEXP has to be copied even
*deep==FALSE*? I made a small test code:

x=runif(10)
> so1=sharedObject(x)
> so2=so1
> so2[1]=10


The last line of the code will call the duplicate function with
*deep==FALSE,* which does not sound correct to me if we don't do a deep
copy of the SEXP.

Best,
Jiefei

On Thu, May 16, 2019 at 3:07 PM Gabriel Becker <gabembecker at gmail.com>
wrote:

> Jiefei,
>
> Inline.
>
> On Thu, May 16, 2019 at 2:30 PM ??? <szwjf08 at gmail.com> wrote:
>
>> Hello Luke and Gabriel,
>>
>> Thank you very much for your quick responses. The explanation of STDVEC
>> is very helpful and I appreciate it! For the wrapper, I have a few new
>> questions.
>>
>>
>> 1. Like Luke said a mutable object is not possible. However, I noticed
>> that there is one extra argument *deep* in the function duplicate. I've
>> googled all the available documentation for ALTREP but I did not find any
>> explanation of it. Could you please give some detail on it?
>>
>
> Deep means in the case of compound/nested structure, e.g., most easily
> illustrative the case of a list in R (or VECSXP in C) , do the elements
> need to be duplicated (deep == TRUE) or *only* the "container" SEXP.
>
> Consider an R list:
>
> x = 1:5
>
> y = 2:20
>
> z= c(TRUE, FALSE)
>
> w = "hi there"
>
> lst = list(a= x, b = y, c =z)
>
> lst2 =lst # NAMED == 2, more than one symbol pointing to
>
> And we want to modify lst like so
>
> lst[[2]] = w
>
> We need to duplicate the "container SEXP", ie the VECSXP, so that lst's
> SEXP and lst2's SEXP point to diferent SEXPs in their second element, but
> we don't need to duplicate any SEXPs that represent the data in any of the
> elements (the SEXPs bound to symbols x, y, z, and w), because none of those
> were modified.
>
> Thus, if deep == FALSE, those element SEXPs are NOT duplicated, just the
> top-level one is. if deep==TRUE, then the element SEXPs are duplicated too,
> because  R decided it neeeded that to happen for some reason.
>
> In terms of implementing an ALTREP class, you can either a) just ignore
> deep and *always* do a deep (ie full) duplication of everything in your
> ALTREP class, or  b) you can pay attention to it and  always create a new
> altrep  but which can potentially - *ONLY in cases where deep==FALSE* -
> not duplicate the SEXPs that make up its alternative representation,
> provided you're careful about then making sure that duplication happens at
> a later time if necessary.
>
> I'd strongly suggest starting with option (a) just to have something
> working and completely safe, then considering if its important enough to
> you to look into (b).
>
> Does that make sense?
>
> Best,
> ~G
>
>
>
>
>>
>> 2.
>>
>>> The first one correctly returns its internal data structure, but the
>>> second
>>> one returns the ALTREP object it wraps since the wrapper itself is an
>>> ALTREP. This behavior is unexpected.
>>
>>
>> I disagree. R_altrep_data1 returns whatever THAT altrep SEXP stores in
>>> its "data1" part. There is no recursion/descent going on, and there
>>> shouldn't be.
>>
>>
>> This is might be a bug since in R release 3.6 it will return the ALTREP
>> instead of the data of the ALTREP. I'm not sure if it has been fixed in
>> 3.7. Here is a simple example:
>>
>> SEXP C_peekSharedMemory(SEXP x) {
>>> while (ALTREP(x)) {
>>> Rprintf("getting data 1\n");
>>> x = R_altrep_data1(x);
>>> }
>>> return(x);
>>> }
>>
>>
>> If calling R_altrep_data1 return the internal data directly, we will only
>> see one message. following my last example
>>
>> > .Internal(inspect(so1))
>>> @0x0000000005e7fbb0 14 REALSXP g0c0 [MARK,NAM(7)]  Share object of type
>>> double
>>> > .Internal(inspect(so2))
>>> @0x0000000005fc5ac0 14 REALSXP g0c0 [MARK,NAM(7)]  wrapper
>>> [srt=-2147483648,no_na=0]
>>>   @0x0000000005e7fbb0 14 REALSXP g0c0 [MARK,NAM(7)]  Share object of
>>> type double
>>> > sm1=peekSharedMemory(so1)
>>> getting data 1
>>> > sm2=peekSharedMemory(so2)
>>> getting data 1
>>> getting data 1
>>
>>
>> We see that so2 call R_altrep_data1 twice to get the internal data. This
>> is very unexpected.
>>
>> Thank you very much for your help again!
>>
>> Best,
>> Jiefei
>>
>>
>>
>> On Thu, May 16, 2019 at 3:47 PM Gabriel Becker <gabembecker at gmail.com>
>> wrote:
>>
>>> Hi Jiefei,
>>>
>>> Thanks for tryingout the ALTREP stuff and letting us know how it is
>>> going. That said I don't think either of these are bugs, per se, but rather
>>> a misunderstanding of the API. Details inline.
>>>
>>>
>>>
>>> On Thu, May 16, 2019 at 11:57 AM ??? <szwjf08 at gmail.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> I have encountered two bugs when using ALTREP APIs.
>>>>
>>>> 1. STDVEC_DATAPTR
>>>>
>>>> From RInternal.h file it has a comment:
>>>>
>>>> /* ALTREP support */
>>>> > void *(STDVEC_DATAPTR)(SEXP x);
>>>>
>>>>
>>>> However, this comment might not be true, the easiest way to verify it
>>>> is to
>>>> define a C++ function:
>>>>
>>>>  void C_testFunc(SEXP a)
>>>> > {
>>>> > STDVEC_DATAPTR(a);
>>>> > }
>>>>
>>>>
>>>> and call it in R via
>>>>
>>>> > a=1:10
>>>> > > C_testFunc(a)
>>>> > Error in C_testFunc(a) : cannot get STDVEC_DATAPTR from ALTREP object
>>>>
>>>>
>>> The STDVEC here refers to the SEXP not being an ALTREP. Anything that
>>> starts with STDVEC should never receive an ALTREP, ie it should only be
>>> called after non-ALTREPness has been confirmed by the surrounding/preceding
>>> code. So this is expected behavior.
>>>
>>>
>>>
>>>
>>>>
>>>>  We can inspect the internal type and call ALTREP function to check if
>>>> it
>>>> is an ALTREP:
>>>>
>>>> > .Internal(inspect(a))
>>>> > @0x000000001b5a3310 13 INTSXP g0c0 [NAM(7)]  1 : 10 (compact)
>>>> > > #This is a wrapper of ALTREP
>>>> > > is.altrep(a)
>>>> > [1] TRUE
>>>>
>>>>
>>>> I've also defined an ALTREP type and it did not work either. I guess
>>>> this
>>>> might be a bug? Or did I miss something?
>>>>
>>>> 2. Wrapper objects in ALTREP
>>>>
>>>> If the duplicate function is defined to return the object itself:
>>>>
>>>> SEXP vector_dulplicate(SEXP x, Rboolean deep) {
>>>> return(x);
>>>> }
>>>>
>>>
>>> So this is a violation of of the contract. <youraltrep>_duplicate *must*
>>> do an actual duplication. Returning the object unduplicated when duplicate
>>> is called is going to have all sorts of unintended negative consequences.
>>> R's internals rely on the fact that a SEXP that has been passed to
>>> DUPLICATE has been duplciated and is safe to modify inplace.
>>>
>>>
>>>
>>>> In R an ALTREP object will behave like an environment
>>>> (pass-by-reference).
>>>> However, if we do something like(pseudo code):
>>>>
>>>> n=100
>>>> > x=runif(n)
>>>> > alt1=createAltrep(x)
>>>> > alt2=alt1
>>>> > alt2[1]=10
>>>> > .Internal(inspect(alt1))
>>>> > .Internal(inspect(alt2))
>>>>
>>>>
>>>> The result would be:
>>>>
>>>> > .Internal(inspect(alt1))
>>>> > @0x00000000156f4d18 14 REALSXP g0c0 [NAM(7)]
>>>> > > .Internal(inspect(alt2 ))
>>>> > @0x00000000156a33e0 14 REALSXP g0c0 [NAM(7)]  wrapper
>>>> > [srt=-2147483648,no_na=0]
>>>> >   @0x00000000156f4d18 14 REALSXP g0c0 [NAM(7)]
>>>>
>>>>
>>>> It seems like the object alt2 automatically gets wrapped by R. Although
>>>> at
>>>> the R level it seems fine because there are no differences between alt1
>>>> and
>>>> alt2, if we define a C function as:
>>>>
>>>
>>> So I'm not sure what is happening here, because it depends on what your
>>> createAltrep function does. R automatically creates wrappers in some cases
>>> but not nearly all (or even very many currently) cases.
>>>
>>>>
>>>> SEXP C_peekSharedMemory(SEXP x) {
>>>> > return(R_altrep_data1(x));
>>>>
>>>> }
>>>>
>>>>
>>>> and call it in R to get the internal data structure of an ALTREP object.
>>>>
>>>> C_peekSharedMemory(alt1)
>>>> > C_peekSharedMemory(alt2)
>>>>
>>>>
>>>> The first one correctly returns its internal data structure, but the
>>>> second
>>>> one returns the ALTREP object it wraps since the wrapper itself is an
>>>> ALTREP. This behavior is unexpected.
>>>
>>>
>>> I disagree. R_altrep_data1 returns whatever THAT altrep SEXP stores in
>>> its "data1" part. There is no recursion/descent going on, and there
>>> shouldn't be.
>>>
>>>
>>>> Since the dulplicate function returns
>>>> the object itself, I will expect alt1 and alt2 should be the same
>>>> object.
>>>>
>>>
>>> Again, this is a violation of the core assumptions of ALTREP that is not
>>> allowed, so I'd argue that any behavior this causes is largely irrelevant
>>> (and a smart part of the much larger set of problems not duplicating when R
>>> told you to duplicate will cause).
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>> Even if they are essentially not the same, calling the same function
>>>> should
>>>> at least return the same result. Other than that, It seems like R does
>>>> not
>>>> always wrap an ALTREP object. If we change n from 100 to 10 and check
>>>> the
>>>> internal again, alt2 will not get wrapped.
>>>
>>>
>>> Right, so this is a misunderstanding (which may be the fault of sparse
>>> documentation on our part);  wrapper is one particular ALTREP class, its
>>> not a fundamental aspect of ALTREPs themselves. Most ALTREP objects do not
>>> have wrappers. See, e.g.,
>>>
>>> > .Internal(inspect(1:4))
>>>
>>> @7fb727d6be50 13 INTSXP g0c0 [NAM(3)]  1 : 4 (compact)
>>>
>>>
>>> That's an ALTREP with no wrapper (a compact sequence). The wrapper
>>> ALTREP class is for attaching metadata (known sortedness, known lack of
>>> NAs) to R vectors. Its primary use currently is on the return value of
>>> sort().
>>>
>>>
>>>> This makes the problem even more
>>>> difficult since we cannot predict when would the wrapper appear.
>>>>
>>>
>>> As currently factored, its not intended that you would be or need to
>>> predict when a wrapper would appear. Using the C API or any R functions
>>> will transparently treat wrapped and non-wrapped objects the same, and any
>>> code you write should hit these API entrypoints so that any code you write
>>> does the same.
>>>
>>> Does that help?
>>>
>>> Best,
>>> ~G
>>>
>>>>
>>>> Here is the source code for the wrapper:
>>>> https://github.com/wch/r-source/blob/trunk/src/main/altclasses.c#L1399
>>>>
>>>> Here is a working example if one can build the sharedObject package from
>>>> https://github.com/Jiefei-Wang/sharedObject
>>>>
>>>> n=100
>>>> > x=runif(n)
>>>> > so1=sharedObject(x,copyOnWrite = FALSE)
>>>> > so2=so1
>>>> > so2[1]=10
>>>> > .Internal(inspect(so1))
>>>> > .Internal(inspect(so2))
>>>>
>>>>
>>>> Here is my session info:
>>>>
>>>> R version 3.6.0 alpha (2019-04-08 r76348)
>>>> > Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>> > Running under: Windows >= 8 x64 (build 9200)
>>>> > Matrix products: default
>>>> > locale:
>>>> > [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>>>> > States.1252
>>>> > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>>> >
>>>> > [5] LC_TIME=English_United States.1252
>>>> > attached base packages:
>>>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>>>> > other attached packages:
>>>> > [1] sharedObject_0.0.99
>>>> > loaded via a namespace (and not attached):
>>>> > [1] compiler_3.6.0 tools_3.6.0    Rcpp_1.0.1
>>>>
>>>>
>>>> Best,
>>>> Jiefei
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>

	[[alternative HTML version deleted]]



[Rd] ALTREP: Bug reports
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