[Rd] some questions about R internal SEXP types

Tomas Kalibera
Tue, 08 Sep 2020 10:08:57 -0000

On 9/8/20 11:47 AM, Dan Kortschak wrote:
> Thanks, Tomas.
>
> This is unfortunate. Calling between Go and C is not cheap; the gc
> implementation of the Go compiler (as opposed to gccgo) uses different
> calling conventions from C and there are checks to ensure that Go
> allocated memory pointers do not leak into C code. For this reason I
> wanted to avoid these if at all possible (I cannot for allocations
> since I don't want to keep tracking changes in how R implements its GC
> and allocation).
>
> However, if SEXP type behaviour of the standard types, and how
> attributes are handled are not highly mobile, I think that what I'm
> doing will be OK - at worst the Go code will panic and result in an R
> error. The necessary interface to R for allocations is only eight
> functions[1].

I am not sure if I understand correctly, but if you were accessing
directly the memory of SEXPs from Go implementation instead of calling
through exported access functions documented in WRE, that would be a
really bad idea. Of course fine for research and experimentation, but
the internal structure can and does change at any time, otherwise we
would not be able to develop nor maintain R. Such direct access
bypassing WRE would likely be a clear case for rejection in CRAN for
this interface and any packages using it, and I hope in other package
repositories as well.

However, I believe the overhead of calling the C-level access functions
R exports should be minimal compared to other overheads. You can't hope,
anyway, for being able to efficiently call tiny functions frequently
between Go and R. This can only work for bigger functions, anyway, and
then the Go-C overhead should not be important.

> Note that there is a lot in WRE that's beyond what I want rgo to be
> able to do (calling in to R from Go for example). In fact, there's just
> a lot in WRE (it's almost 3 times the length of the Go language spec
> and memory model reference combined). The issues around weak references
> and external pointers are not something that I want to deal with;
> working with that kind of object is not idiomatic for Go (in fact
> without using C.malloc, R external pointers from Go would be forbidden
> by the Go runtime) and I would not expect that they are likely to be
> used by people writing extensions for R in Go.

Sure, I think it is perfectly fine to cover only a subset, if that is
already useful to write some extensions in Go. Maintenance would be
easiest if Go programs didn't call back into the R runtime at all, so
fewer calls the better for maintenance.

Best
Tomas

>
> Dan
>
> [1]
>
>
>
https://github.com/rgonomic/rgo/blob/2ce7717c85516bbfb94d0b5c7ef1d9749dd1f817/sexp/r_internal.go#L86-L118
>
> On Tue, 2020-09-08 at 11:07 +0200, Tomas Kalibera wrote:
>> The general principle is that R packages are only allowed to use what
>> is
>> documented in the R help (? command) and in Writing R Extensions. The
>> former covers what is allowed from R code in extensions, the latter
>> mostly what is allowed from C code in extensions (with some
>> references
>> to Fortran).
>>
>> If you are implementing a Go interface for writing R packages, such
>> Go
>> interface should thus only use what is in the R help and in Writing R
>> Extensions. Otherwise, packages would not be able to use such
>> interface.
>>
>> What is described in R Internals is for understanding the internal
>> structure of R implementation itself, so for development of R itself,
>> it
>> could help indeed also debugging of R itself and in some cases
>> debugging
>> or performance analysis of extensions. R Internals can help in giving
>> an
>> intuition, but when people are implementing R itself, they also need
>> to
>> check the code. R Internals does not describe any interface for
>> external
>> code, if it states any constraints about say pairlists, etc, take it
>> as
>> an intuition for what has been intended and probably holds or held at
>> some level of abstraction, but you need to check the source code for
>> the
>> details, anyway (e.g., at some very low level CAR and CDR can be any
>> SEXP or R_NilValue, locally in some functions even C NULL).
>> Internally,
>> some C code uses C NULL SEXPs, but it is rare and local, and again,
>> only
>> the interface described in Writing R Extensions is for external use.
>>
>> WRE speaks about "R NULL", "R NULL object" or
"C NULL" in some cases
>> to
>> avoid confusion, e.g. for values types as "void *". SEXPs
that
>> packages
>> obtain using the interface in WRE should not be C NULL, only R NULL
>> (R_NilValue). External pointers can become C NULL and this is
>> documented
>> in WRE 5.13.
>>
>> Best
>> Tomas
>>
>> On 9/6/20 3:44 AM, Dan Kortschak via R-devel wrote:
>>> Hello,
>>>
>>> I am writing an R/Go interoperability tool[1] that work similarly
>>> to
>>> Rcpp; the tool takes packages written in Go and performs the
>>> necessary
>>> Go type analysis to wrap the Go code with C and R shims that allow
>>> the
>>> Go code to then be called from R. The system is largely complete
>>> (with
>>> the exception of having a clean approach to handling generalised
>>> attributes in the easy case[2] - the less hand holding case does
>>> handle
>>> these). Testing of some of the code is unfortunately lacking
>>> because of
>>> the difficulties of testing across environments.
>>>
>>> To make the system flexible I have provided an (intentionally
>>> incomplete) Go API into the R internals which allows reasonably Go
>>> type-safe interaction with SEXP values (Go does not have unions, so
>>> this is uglier than it might be otherwise and unions are faked with
>>> Go
>>> interface values). For efficiency reasons I've avoided using R
>>> internal
>>> calls where possible (accessors are done with Go code directly, but
>>> allocations are done in R's C code to avoid having to duplicate
the
>>> garbage collection mechanics in Go with the obvious risks of error
>>> and
>>> possible behaviour skew in the future).
>>>
>>> In doing this work I have some questions that I have not been able
>>> to
>>> find answers for in the R-ints doc or hadley/r-internals.
>>>
>>>      1. In R-ints, the LISTSXP SEXP type CDR is said to hold
>>> "usually"
>>>         LISTSXP or NULL. What does the "usually" mean
here? Is it
>>> possible
>>>         for the CDR to hold values other than LISTSXP or NULL, and
>>> is
>>>         this NULL NILSXP or C NULL? I assume that the CAR can hold
>>> any type
>>>         of SEXP, is this correct?
>>>      2. The LANGSXP and DOTSXP types are lists, but the R-ints
>>> comments on
>>>         them do not say whether the CDR of one of these lists is
the
>>> same at
>>>         the head of the list of devolves to a LISTSXP. Looking
>>> through the
>>>         code suggests to me that functions that allocate these two
>>> types
>>>         allocate a LISTSXP and then change only the head of the
list
>>> to be
>>>         the LANGSXP or DOTSXP that's required, meaning that the
tail
>>> of the
>>>         list is all LISTSXP. Is this correct?
>>>
>>> The last question is more a question of interest in design
>>> strategy,
>>> and the answer may have been lost to time. In order to reduce the
>>> need
>>> to go through Go's interface assertions in a number of cases I
have
>>> decided to reinterpret R_NilValue to an untyped Go nil (this is
>>> important for example in list traversal where the CDR can
>>> (hopefully)
>>> be only one of two types LISTSXP or NILSXP; in Go this would
>>> require a
>>> generalised SEXP return, but by doing this reinterpretation I can
>>> return a *List pointer which may be nil, greatly simplifying the
>>> code
>>> and improving the performance). My question her is why a singleton
>>> null
>>> value was chosen to be represented as a fully allocated SEXP value
>>> rather than just a C NULL. Also, whether C NULL is used to any
>>> great
>>> extent within the internal code. Note that the Go API provides a
>>> mechanism to easily reconvert the nil's used back to a
R_NilValue
>>> when
>>> returning from a Go function[3].
>>>
>>> thanks
>>> Dan Kortschak
>>>
>>> [1]https://github.com/rgonomic/rgo
>>> [2]https://github.com/rgonomic/rgo/issues/1
>>> [3]
>>>
> https://pkg.go.dev/github.com/rgonomic/rgo/sexp?tab=doc#Value.Export
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>