I agree we should be using R_xlen_t here. As always, PRs are welcome.
You might want to file this at https://github.com/RcppCore/Rcpp/issues
just so it doesn't get lost.
Thanks,
Kevin
On Tue, Nov 6, 2018 at 11:23 PM Qiang Kou <q...@qkou.info> wrote:
>
> Hi, William,
>
> Can you give us a small piece of code to reproduce the error? That will ease
> our discussion.
>
> Best,
>
> KK
>
> On Tue, Nov 6, 2018 at 10:46 PM William Nolan <w...@landale.net> wrote:
>>
>> Hi all,
>>
>> Longtime user and lurker here.
>>
>> I got "index error" thrown by Rcpp when trying to subset a matrix with width
>> * height == 644764 * 3776 greater than MAXINT:
>>
>> Allocating 647764 x 3776 matrix...
>> Catchpoint 1 (exception thrown), 0x00007ffff4baa920 in __cxa_throw () from
>> /usr/lib64/libstdc++.so.6
>> #1 0x0000000000473a05 in Rcpp::stop<>(char const*) (fmt=0x7fffe7bc3545
>> "index error")
>> at
>> /home/nolanw/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:52
>> 52 throw Rcpp::exception( tfm::format(fmt,
>> std::forward<Args>(args)... ).c_str() );
>> (gdb) down
>> #0 0x00007ffff4baa920 in __cxa_throw () from /usr/lib64/libstdc++.so.6
>> (gdb) up
>> #1 0x0000000000473a05 in Rcpp::stop<>(char const*) (fmt=0x7fffe7bc3545
>> "index error")
>> at
>> /home/nolanw/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:52
>> 52 throw Rcpp::exception( tfm::format(fmt,
>> std::forward<Args>(args)... ).c_str() );
>> (gdb) up
>> #2 0x00007fffe7bb75a6 in Rcpp::SubsetProxy<14, Rcpp::PreserveStorage, 13,
>> true, Rcpp::Vector<13, Rcpp::PreserveStorage> >::check_indices
>> (this=0x7fffffffc450, x=0x13f9920,
>> n=3751, size=-1849010432) at
>> /home/nolanw/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include/Rcpp/vector/:138
>> 138 stop("index error");
>> (gdb) up
>> #3 0x00007fffe7bb6a3c in Rcpp::SubsetProxy<14, Rcpp::PreserveStorage, 13,
>> true, Rcpp::Vector<13, Rcpp::PreserveStorage> >::get_indices
>> (this=0x7fffffffc450, t=...)
>> at
>> /home/nolanw/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include/Rcpp/vector/Subsetter.h:149
>> 149 check_indices(ptr, rhs_n, lhs_n);
>> (gdb) l
>> 144 #endif
>> 145
>> 146 void get_indices( traits::identity< traits::int2type<INTSXP> > t
>> ) {
>> 147 indices.reserve(rhs_n);
>> 148 int* ptr = INTEGER(rhs);
>> 149 check_indices(ptr, rhs_n, lhs_n);
>> 150 for (int i=0; i < rhs_n; ++i) {
>> 151 indices.push_back( rhs[i] );
>> 152 }
>> 153 indices_n = rhs_n;
>>
>> As we can see from the stack trace and below, lhs.size() is negative when
>> cast to int:
>>
>> (gdb) p (int)(lhs.size())
>> $12 = -1849010432
>>
>> This is all coming from the assignment (via operator []) of the subsetting
>> of one matrix to another matrix's subset:
>>
>> (static_cast<NumericVector&>(mat))[lhsI] =
>> (static_cast<NumericVector&>(signals))[rhsI];
>>
>> (lhsI and rhsI are IntegerVector's)
>>
>> Now, setting aside whether I *should* be doing that -- what I *do* see in
>> Subsetter.h (including what I understand to be the most recent version,
>> 1.0.0 from github) is the use of int for indices all over the place in this
>> file, including in the member variable:
>>
>> std::vector<int> indices;
>>
>> Is there any reason why the indices that Subsetter uses internally shouldn't
>> be size_t or an equivalently capable type like R_xlen_t?
>> For example, Subsetter's check_indices function takes int's as arguments,
>> while Vector's size method returns R_xlen_t.
>>
>> I'll change my code to manually copy elements via operator() using the
>> row/column arguments for now. Seems like Subsetter is maybe not quite ready
>> for prime time.
>>
>>
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