R devel - Jun 2024 - [External] Re: changes in R-devel and zero-extent objects in Rcpp

The ASAN errors occur *even if the zero-length object is not actually 
accessed*/is used in a perfectly correct manner, i.e. it's perfectly 
legal in base R to define `m <- numeric(0)` or `m <- matrix(nrow = 0, 
ncol = 0)`, whereas doing the equivalent in Rcpp will (now) lead to an 
ASAN error.

   i.e., these are *not* previously cryptic out-of-bounds accesses that 
are now being revealed, but instead sensible and previously legal 
definitions of zero-length objects that are now causing problems.

    I'm pretty sure I'm right about this, but it's absolutely
possible
that I'm just confused at this point; I don't have a super-simple 
example to show you at the moment. The closest is this example by Mikael 
Jagan: https://github.com/lme4/lme4/issues/794#issuecomment-2155093049

   which shows that if x is a pointer to a zero-length vector (in plain 
C++ for R, no Rcpp is involved), DATAPTR(x) and REAL(x) evaluate to 
different values.

   Mikael further points out that "Rcpp seems to cast a (void *) 
returned by DATAPTR to (double *) when constructing a Vector<REALSXP> 
from a SEXP, rather than using the (double *) returned by REAL." So 
perhaps R-core doesn't want to guarantee that these operations give 
identical answers, in which case Rcpp will have to change the way it 
does things ...

   cheers
    Ben



On 2024-06-08 6:39 p.m., Kevin Ushey wrote:
> IMHO, this should be changed in both Rcpp and downstream packages:
> 
> 1. Rcpp could check for out-of-bounds accesses in cases like these, and 
> emit an R warning / error when such an access is detected;
> 
> 2. The downstream packages unintentionally making these out-of-bounds 
> accesses should be fixed to avoid doing that.
> 
> That is, I think this is ultimately a bug in the affected packages, but 
> Rcpp could do better in detecting and handling this for client packages 
> (avoiding a segfault).
> 
> Best,
> Kevin
> 
> 
> On Sat, Jun 8, 2024, 3:06?PM Ben Bolker <bbolker at gmail.com 
> <mailto:bbolker at gmail.com>> wrote:
> 
> 
>      ? ? A change to R-devel (SVN r86629 or
>    
https://github.com/r-devel/r-svn/commit/92c1d5de23c93576f55062e26d446feface07250
<https://github.com/r-devel/r-svn/commit/92c1d5de23c93576f55062e26d446feface07250>
>     has changed the handling of pointers to zero-length objects, leading to
>     ASAN issues with a number of Rcpp-based packages (the commit message
>     reads, in part, "Also define STRICT_TYPECHECK when compiling
>     inlined.c.")
> 
>      ? ?I'm interested in discussion from the community.
> 
>      ? ?Details/diagnosis for the issues in the lme4 package are here:
>     https://github.com/lme4/lme4/issues/794
>     <https://github.com/lme4/lme4/issues/794>, with a bit more
discussion
>     about how zero-length objects should be handled.
> 
>      ? ?The short(ish) version is that r86629 enables the
>     CATCH_ZERO_LENGTH_ACCESS definition. This turns on the CHKZLN macro
>    
<https://github.com/r-devel/r-svn/blob/4ef83b9dc3c6874e774195d329cbb6c11a71c414/src/main/memory.c#L4090-L4104
<https://github.com/r-devel/r-svn/blob/4ef83b9dc3c6874e774195d329cbb6c11a71c414/src/main/memory.c#L4090-L4104>>,
>     which returns a trivial pointer (rather than the data pointer that
>     would
>     be returned in the normal control flow) if an object has length 0:
> 
>     /* Attempts to read or write elements of a zero length vector will
>      ? ? result in a segfault, rather than read and write random memory.
>      ? ? Returning NULL would be more natural, but Matrix seems to assume
>      ? ? that even zero-length vectors have non-NULL data pointers, so
>      ? ? return (void *) 1 instead. Zero-length CHARSXP objects still have
a
>      ? ? trailing zero byte so they are not handled. */
> 
>      ? ?In the Rcpp context this leads to an inconsistency, where `REAL(x)`
>     is a 'real' external pointer and `DATAPTR(x)` is 0x1, which in
turn
>     leads to ASAN warnings like
> 
>     runtime error: reference binding to misaligned address 0x000000000001
>     for type 'const double', which requires 8 byte alignment
>     0x000000000001: note: pointer points here
> 
>      ? ? I'm in over my head and hoping for insight into whether this
>     problem
>     should be resolved by changing R, Rcpp, or downstream Rcpp packages ...
> 
>      ? ?cheers
>      ? ? Ben Bolker
> 
>     ______________________________________________
>     R-devel at r-project.org <mailto:R-devel at r-project.org>
mailing list
>     https://stat.ethz.ch/mailman/listinfo/r-devel
>     <https://stat.ethz.ch/mailman/listinfo/r-devel>
> 
-- 
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
 > E-mail is sent at my convenience; I don't expect replies outside of 
working hours.

On Sat, 8 Jun 2024, Ben Bolker wrote:
>  The ASAN errors occur *even if the zero-length object is not actually 
> accessed*/is used in a perfectly correct manner, i.e. it's perfectly
legal in
> base R to define `m <- numeric(0)` or `m <- matrix(nrow = 0, ncol =
0)`,
> whereas doing the equivalent in Rcpp will (now) lead to an ASAN error.
>
>  i.e., these are *not* previously cryptic out-of-bounds accesses that are 
> now being revealed, but instead sensible and previously legal definitions
of
> zero-length objects that are now causing problems.
>
>   I'm pretty sure I'm right about this, but it's absolutely
possible that
> I'm just confused at this point; I don't have a super-simple
example to show
> you at the moment. The closest is this example by Mikael Jagan: 
> https://github.com/lme4/lme4/issues/794#issuecomment-2155093049
>
>  which shows that if x is a pointer to a zero-length vector (in plain C++ 
> for R, no Rcpp is involved), DATAPTR(x) and REAL(x) evaluate to different 
> values.
>
>  Mikael further points out that "Rcpp seems to cast a (void *)
returned by
> DATAPTR to (double *) when constructing a Vector<REALSXP> from a
SEXP, rather
> than using the (double *) returned by REAL." So perhaps R-core
doesn't want
> to guarantee that these operations give identical answers, in which case
Rcpp
> will have to change the way it does things ...
It looks like REAL and friends should also get this check, but it's
not high priority at this point, at least to me. DATAPTR has been
using this check for a while in a barrier build, so you might want to
test there as well. I expect we will activate more integrity checks
from the barrier build on the API client side as things are tidied up.

However: DATAPTR is not in the API and can't be at least in this form:
It allows access to a writable pointer to STRSXP and VECSXP data and
that is too dangerous for memory manager integrity. I'm not sure
exactly how this will be resolve, but be prepared for changes.

Best,

luke
>
>  cheers
>   Ben
>
>
>
> On 2024-06-08 6:39 p.m., Kevin Ushey wrote:
>> IMHO, this should be changed in both Rcpp and downstream packages:
>> 
>> 1. Rcpp could check for out-of-bounds accesses in cases like these, and
>> emit an R warning / error when such an access is detected;
>> 
>> 2. The downstream packages unintentionally making these out-of-bounds 
>> accesses should be fixed to avoid doing that.
>> 
>> That is, I think this is ultimately a bug in the affected packages, but
>> Rcpp could do better in detecting and handling this for client packages
>> (avoiding a segfault).
>> 
>> Best,
>> Kevin
>> 
>> 
>> On Sat, Jun 8, 2024, 3:06?PM Ben Bolker <bbolker at gmail.com 
>> <mailto:bbolker at gmail.com>> wrote:
>> 
>>
>>      ? ? A change to R-devel (SVN r86629 or
>>    
https://github.com/r-devel/r-svn/commit/92c1d5de23c93576f55062e26d446feface07250
>>
<https://github.com/r-devel/r-svn/commit/92c1d5de23c93576f55062e26d446feface07250>
>>     has changed the handling of pointers to zero-length objects,
leading to
>>     ASAN issues with a number of Rcpp-based packages (the commit
message
>>     reads, in part, "Also define STRICT_TYPECHECK when compiling
>>     inlined.c.")
>>
>>      ? ?I'm interested in discussion from the community.
>>
>>      ? ?Details/diagnosis for the issues in the lme4 package are here:
>>     https://github.com/lme4/lme4/issues/794
>>     <https://github.com/lme4/lme4/issues/794>, 
>> with a bit more discussion
>>     about how zero-length objects should be handled.
>>
>>      ? ?The short(ish) version is that r86629 enables the
>>     CATCH_ZERO_LENGTH_ACCESS definition. This turns on the CHKZLN macro
>>    
<https://github.com/r-devel/r-svn/blob/4ef83b9dc3c6874e774195d329cbb6c11a71c414/src/main/memory.c#L4090-L4104
>>
<https://github.com/r-devel/r-svn/blob/4ef83b9dc3c6874e774195d329cbb6c11a71c414/src/main/memory.c#L4090-L4104>>,
>>     which returns a trivial pointer (rather than the data pointer that
>>     would
>>     be returned in the normal control flow) if an object has length 0:
>>
>>     /* Attempts to read or write elements of a zero length vector will
>>      ? ? result in a segfault, rather than read and write random
memory.
>>      ? ? Returning NULL would be more natural, but Matrix seems to
assume
>>      ? ? that even zero-length vectors have non-NULL data pointers, so
>>      ? ? return (void *) 1 instead. Zero-length CHARSXP objects still
have
>> a
>>      ? ? trailing zero byte so they are not handled. */
>>
>>      ? ?In the Rcpp context this leads to an inconsistency, where
`REAL(x)`
>>     is a 'real' external pointer and `DATAPTR(x)` is 0x1, which
in turn
>>     leads to ASAN warnings like
>>
>>     runtime error: reference binding to misaligned address
0x000000000001
>>     for type 'const double', which requires 8 byte alignment
>>     0x000000000001: note: pointer points here
>>
>>      ? ? I'm in over my head and hoping for insight into whether
this
>>     problem
>>     should be resolved by changing R, Rcpp, or downstream Rcpp packages
...
>>
>>      ? ?cheers
>>      ? ? Ben Bolker
>>
>>     ______________________________________________
>>     R-devel at r-project.org <mailto:R-devel at r-project.org>
mailing list
>>     https://stat.ethz.ch/mailman/listinfo/r-devel
>>     <https://stat.ethz.ch/mailman/listinfo/r-devel>
>> 
>
>
-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu/