[Rcpp-devel] Possible regression in R-3.2.3 or Rcpp 0.12.3

[Qiang Kou]

Another thing confused me is the segfault only happens when the
IntegerVector is significantly long.

Best,

KK

On Sat, Jan 30, 2016 at 2:57 AM, Kevin Ushey <kevinushey at gmail.com> wrote:

> Hmm, I have one thought: we try to re-use the indices from an
> IntegerVector, but the type here is actually a sugar type:
>
>     Rcpp::SubsetProxy<13, Rcpp::PreserveStorage, 13, true,
>     Rcpp::sugar::Minus_Vector_Primitive<13, true, Rcpp::Vector<13,
>     Rcpp::PreserveStorage> > >::get_vec (this=<optimized out>)
>
> Ie, we access the indices with `INTEGER(x)`, but perhaps those indices
> have not actually been properly materialized when we attempt to
> perform the subset?
>
> But then, a simple test case with `x[y - 1]` with `x` and `y` both
> being integer vectors seems to work just fine. So I am a bit confused.
>
> On Fri, Jan 29, 2016 at 3:16 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
> >
> > On 29 January 2016 at 17:55, Qiang Kou wrote:
> > | Hi, Paul, can you try my fork of Rcpp? You can install it by the line
> below:
> > |
> > | devtools::install_github("thirdwing/Rcpp", ref = "subsetter")
> > |
> > | This fixed the segfault on my Ubuntu machine.
> >
> > Yay. Nice work!
> >
> > | The difference can be found from [1].
> >
> > Nice and concise.
> >
> > | In subsetter, if an IntegerVector passed in, we will try to reuse it.
> This led
> > | to a segfault in this case, which I don't know why.
> > |
> > | Dirk and Kevin, do you have any thoughts on it?
> >
> > Not really, but happy to give this the full reverse-dependency check
> > treatment so that we can merge it.
> >
> > Dirk
> >
> >
> > | Best wishes,
> > |
> > | KK
> > |
> > | [1] https://github.com/thirdwing/Rcpp/commit/
> > | 216c5220bcb84778a656b3496d0f1803b973ef61
> > |
> > |
> > | On Fri, Jan 29, 2016 at 3:00 PM, Qiang Kou <qkou at umail.iu.edu> wrote:
> > |
> > |
> > |     Hi, Kevin, I was also trying to track this down yesterday.
> > |
> > |     From the debugging info below, indices_n is not equal to length of
> indices,
> > |     which I don't quite understand.
> > |
> > |     Program received signal SIGSEGV, Segmentation fault.
> > |
> > |     0x00007ffff2ed5c4e in Rcpp::SubsetProxy<13, Rcpp::PreserveStorage,
> 13,
> > |     true, Rcpp::sugar::Minus_Vector_Primitive<13, true,
> Rcpp::Vector<13,
> > |     Rcpp::PreserveStorage> > >::get_vec (this=this at entry
> =0x7fffffff79a0)
> > |
> > |         at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/vector/
> > |     Subsetter.h:200
> > |
> > |     199             output[i] = lhs[ indices[i] ];
> > |
> > |     (gdb) p i
> > |
> > |     $1 = 33622
> > |
> > |     (gdb) p indices[i]
> > |
> > |     Cannot access memory at address 0x34c6e000
> > |
> > |     (gdb) p indices_n
> > |
> > |     $2 = 9594546
> > |
> > |
> > |     On Fri, Jan 29, 2016 at 2:29 PM, Dirk Eddelbuettel <edd at debian.org>
> wrote:
> > |
> > |
> > |         On 29 January 2016 at 11:27, Kevin Ushey wrote:
> > |         | When I add some debug printing to the associated
> subscripting line
> > |         | (https://github.com/awalker89/openxlsx/blob/
> > |
>  b92bb3acdd6ea759be928c298c6faeef2f26fa3e/src/cppFunctions.cpp#L2608),
> > |         | I see:
> > |         |
> > |         |    colNumbers.size(): 98,03,150
> > |         |    charCols.size(): 95,94,546
> > |         |
> > |         | It looks to me like the package is erroneously attempting to
> subset
> > |         | vectors of different sizes, causing out-of-bounds reads.
> > |
> > |         Nice work.
> > |
> > |         | Unfortunately, Rcpp is not detecting or warning about this...
> > |         |
> > |         | Either way, I believe this is a bug in the openxlsx package,
> but Rcpp
> > |         | should be checking / reporting this.
> > |
> > |         With (Rcpp)Armadillo you do have an option of turning this
> on/off. With
> > |         Rcpp
> > |         alone not quite.
> > |
> > |         Dirk
> > |
> > |         --
> > |         http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
> > |         _______________________________________________
> > |         Rcpp-devel mailing list
> > |         Rcpp-devel at lists.r-forge.r-project.org
> > |
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> > |
> > |
> > |
> > |
> > |     --
> > |     Qiang Kou
> > |     qkou at umail.iu.edu
> > |     School of Informatics and Computing, Indiana University
> > |
> > |
> > |
> > |
> > |
> > | --
> > | Qiang Kou
> > | qkou at umail.iu.edu
> > | School of Informatics and Computing, Indiana University
> > |
> >
> > --
> > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>



-- 
Qiang Kou
qkou at umail.iu.edu
School of Informatics and Computing, Indiana University
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