[Rd] [External] Possible ALTREP bug

Fri May 28 23:15:33 CEST 2021

Since the INTEGER_ELT, REAL_ELT, etc, functions are fairly new it may
be possible to check that places where they are used allow for them to
allocate. I have fixed the one that got caught by Gabor's example, and
a rchk run might be able to pick up others if rchk knows these could
allocate. (I may also be forgetting other places where the _ELt
methods are used.)  Fixing all call sites for REAL, INTEGER, etc, was
never realistic so there GC has to be suspended during the method
call, and that is done in the dispatch mechanism.

The bigger problem is jumps from inside things that existing code
assumes will not do that. Catching those jumps is possible but
expensive; doing anything sensible if one is caught is really not
possible.

Best,

luke

On Fri, 28 May 2021, Gabriel Becker wrote:

> Hi Jim et al,
> Just to hopefully add a bit to what Luke already answered, from what I am
> recalling looking back at that bioconductor thread Elt methods are used in
> places where there are hard implicit assumptions that no garbage collection
> will occur (ie they are called on things that aren't PROTECTed), and beyond
> that, in places where there are hard assumptions that no error (longjmp)
> will occur. I could be wrong, but I don't know that suspending garbage
> collection would protect from the second one. Ie it is possible that an
> error *ever* being raised from R code that implements an elt method could
> cause all hell to break loose.
> 
> Luke or Tomas Kalibera would know more.
> 
> I was disappointed that implementing ALTREPs in R code was not in the cards
> (it was in my original proposal back in 2016 to the DSC) but I trust Luke
> that there are important reasons we can't safely allow that.
> 
> Best,
> ~G
> 
> On Fri, May 28, 2021 at 8:31 AM Jim Hester <james.f.hester using gmail.com> wrote:
>       From reading the discussion on the Bioconductor issue tracker it
>       seems like
>       the reason the GC is not suspended for the non-string ALTREP Elt
>       methods is
>       primarily due to performance concerns.
>
>       If this is the case perhaps an additional flag could be added to
>       the
>       `R_set_altrep_*()` functions so ALTREP authors could indicate if
>       GC should
>       be halted when that particular method is called for that
>       particular ALTREP
>       class.
>
>       This would avoid the performance hit (other than a boolean
>       check) for the
>       standard case when no allocations are expected, but allow
>       authors to
>       indicate that R should pause GC if needed for methods in their
>       class.
>
>       On Fri, May 28, 2021 at 9:42 AM <luke-tierney using uiowa.edu> wrote:
>
>       > integer and real Elt methods are not expected to allocate. You
>       would
>       > have to suspend GC to be able to do that. This currently can't
>       be done
>       > from package code.
>       >
>       > Best,
>       >
>       > luke
>       >
>       > On Fri, 28 May 2021, Gábor Csárdi wrote:
>       >
>       > > I have found some weird SEXP corruption behavior with
>       ALTREP, which
>       > > could be a bug. (Or I could be doing something wrong.)
>       > >
>       > > I have an integer ALTREP vector that calls back to R from
>       the Elt
>       > > method. When this vector is indexed in a lapply(), its first
>       element
>       > > gets corrupted. Sometimes it's just a type change to
>       logical, but
>       > > sometimes the corruption causes a crash.
>       > >
>       > > I saw this on macOS from R 3.5.3 to 4.2.0. I created a small
>       package
>       > > that demonstrates this:
>       https://github.com/gaborcsardi/redfish
>       > >
>       > > The R callback in this package calls
>       `loadNamespace("Matrix")`, but
>       > > the same crash happens for other packages as well, and
>       sometimes it
>       > > also happens if I don't load any packages at all. (But that
>       example
>       > > was much more complicated, so I went with the package
>       loading.)
>       > >
>       > > It is somewhat random, and sometimes turning off the JIT
>       avoids the
>       > > crash, but not always.
>       > >
>       > > Hopefully I am just doing something wrong in the ALTREP code
>       (see
>       > >
>       https://github.com/gaborcsardi/redfish/blob/main/src/test.c),
>       and it
>       > > is not actually a bug.
>       > >
>       > > Thanks,
>       > > Gabor
>       > >
>       > > ______________________________________________
>       > > R-devel using r-project.org mailing list
>       > > 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 using uiowa.edu
>       > Iowa City, IA 52242                 WWW: 
>       http://www.stat.uiowa.edu
>       > ______________________________________________
>       > R-devel using r-project.org mailing list
>       > https://stat.ethz.ch/mailman/listinfo/r-devel
>       >
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>

-- 
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 using uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu