I got another error when using the Matrix.column() function, as in the
code below:
#include <Rcpp.h>
#include "array.cpp"
// [[Rcpp::export]]
Rcpp::IntegerMatrix makeMat(int nrow=18, int ncol=136633572){
Rcpp::IntegerMatrix mat(nrow, ncol);
for (int i = 0; i < ncol; ++i) {
Rcpp::MatrixColumn<INTSXP> col = mat.column(i);
for (int j = 0; j < nrow; ++j){
col[j] = 1;
}
}
return mat;
}
Then in R:
> library(Rcpp)
> sourceCpp("makeMat.cpp")
> mat <- makeMat()
*** caught segfault ***
address 0x7f4c1e825088, cause 'memory not mapped'
Traceback:
1: .Primitive(".Call")(<pointer: 0x7f5068e0cee0>, nrow, ncol)
2: makeMat()
If I had to guess, the column function is doing the multiplication
i*nrow and storing it as an int, which overflows when i is big. I am
sorry that I cannot point to the Rcpp code where this happens and
propose the fix, I am sitting on a chair with my laptop on my legs,
not quite convenient for programming :D.
Best,
Alessandro
On Sun, Nov 1, 2015 at 7:35 PM, Alessandro Mammana
<mamm...@molgen.mpg.de> wrote:
> As Sean O'Riordain correctly pointed out, I used the install_github
> command improperly. Doing
>
> devtools::install_github("RcppCore/Rcpp")
>
> works and the big matrix is allocated correctly.
>
> Thanks for the help and for the great work you are doing!
> Ale
>
> On Sun, Nov 1, 2015 at 6:30 PM, Alessandro Mammana
> <mamm...@molgen.mpg.de> wrote:
>> It's great that R and Rcpp have support for long vectors! that makes
>> my life so much easier!
>>
>> So I installed Rcpp version 0.12.1 and the error is still there (see
>> end of the email). If I interpret the commit history correctly, the
>> commit that fixes the bug was done shortly after the 0.12.1 release
>> right? Is there an easy way of getting the latest version of the
>> master branch?
>> I tried:
>>
>> devtools::install_github("https://github.com/RcppCore/Rcpp";)
>>
>> But I got:
>>
>> Error in username %||% getOption("github.user") %||% stop("Unknown
>> username.") :
>> Unknown username.
>>
>>> sourceCpp("makeMat.cpp")
>>> makeMat(18, 136633572)
>> Error in .Primitive(".Call")(<pointer: 0x7f57d1c73ee0>, nrow, ncol) :
>> negative length vectors are not allowed
>>> sesssionInfo()
>> Error: could not find function "sesssionInfo"
>>> sessionInfo()
>> R version 3.2.0 (2015-04-16)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> Running under: MarIuX64 2.0 GNU/Linux 2010-2012
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
>> [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
>> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] Rcpp_0.12.1
>>
>> On Sun, Nov 1, 2015 at 3:37 PM, Florian Plaza Oñate
>> <florian.pl...@jouy.inra.fr> wrote:
>>> The bug is probably fixed by this commit:
>>> https://github.com/RcppCore/Rcpp/commit/eb069bf5c20aaa4d38e0ca2897bf04e956cb8c4c
>>>
>>>
>>> Le 31/10/2015 20:08, Alessandro Mammana a écrit :
>>>>
>>>> Dear All,
>>>> When creating a large matrix with the follwing code:
>>>>
>>>> #include <Rcpp.h>
>>>> // [[Rcpp::export]]
>>>> Rcpp::IntegerMatrix makeMat(int nrow, int ncol){
>>>> Rcpp::IntegerMatrix mat(nrow, ncol);
>>>> return mat;
>>>> }
>>>>
>>>> I get the error:
>>>>
>>>> Error in .Primitive(".Call")(<pointer: 0x7f86936d3ea0>, nrow, ncol) :
>>>> negative length vectors are not allowed
>>>>
>>>> Where nrow*ncol is a very large number (about 3*10^9). I understand
>>>> that such a number cannot be represented by an int type, but this does
>>>> not seem to be a problem when in R I do:
>>>>
>>>>> mat <- matrix(0, nrow=nrow, ncol=ncol)
>>>>
>>>>
>>>> Questions:
>>>> 1. why is the behaviour different between R and Rcpp in the allocation
>>>> of a matrix?
>>>> 2. In a 64 bits machine, what is actually the maximum allowed length
>>>> of a vector/matrix? does the length of a vector/matrix need to be
>>>> represented by an int?
>>>>
>>>> Thanks a lot and best regards,
>>>> Alessandro
>>>>
>>>
>>
>>
>>
>> --
>> Alessandro Mammana, PhD Student
>> Max Planck Institute for Molecular Genetics
>> Ihnestraße 63-73
>> D-14195 Berlin, Germany
>
>
>
> --
> Alessandro Mammana, PhD Student
> Max Planck Institute for Molecular Genetics
> Ihnestraße 63-73
> D-14195 Berlin, Germany
--
Alessandro Mammana, PhD Student
Max Planck Institute for Molecular Genetics
Ihnestraße 63-73
D-14195 Berlin, Germany
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