[Rcpp-devel] A tough RcppArmadillo Error; address(nil) cause 'unknown' in R
Qiang Kou
qkou at umail.iu.edu
Mon Jul 10 00:38:08 CEST 2017
Hi, professor,
I think the problem is in ge-r. cpp, you forgot to call *initialize*.
The error has nothing to do with Rcpp.
Best,
KK
On Tue, Jul 4, 2017 at 2:45 AM, 井澤 毅 <a-izawa at mail.ecc.u-tokyo.ac.jp> wrote:
> Sorry, I forgot the attached file.
> On 2017/07/04 18:43, 井澤 毅 wrote:
>
> Dear KK,
>
> Thanks for your kind reply.
>
> I am afraid that one of the input file is very heavy, this time but I am
> sending a ZIP file including all.
>
> Please make v30 package using install.simulate_R_1.r and then
> install.simulate_R_2.r. Then, try ge-r_test.r, please.
>
> To make the v30 package, we need ge-r.cpp, ge-model.cpp, ge-model.h,
> ge-obs.cpp, ge-obs.h, ge-range.h.
>
> As the input file, we need var.mat.all matrix data in R and
> obs.Os01g0182600_g1.nc file in the directry.
>
> Then, you will see the error I have been suffering from for a month.
>
> The obs.Os01g0182600_g1.nc file is a file containing environmental
> fluctuation data.
>
> Best,
>
> Takeshi
>
> On 2017/07/04 5:40, Qiang Kou wrote:
>
> Hi, I am afraid the example you provided is not a reproducible example.
>
> First, we don't know the content of ge-model.h. Second, we don't know
> which input will trigger the fault.
>
> Please provide a reproducible example if you really want to get help.
>
> Best,
>
> KK
>
> On Sat, Jul 1, 2017 at 11:06 AM, 井澤 毅 <a-izawa at mail.ecc.u-tokyo.ac.jp>
> wrote:
>
>> Dear rcpp-devel at lists.r-forge.r-project.org,
>>
>> Sorry for bothering you much, but do me a favor please. Please help me
>> some.
>>
>> I am just a molecular biologist working on plants. Thus, I am still a
>> newcomer in this field.
>>
>> Recently, I have been working with a script using RcppArmadillo, This has
>> helped me a lot. However, after updating the system in our institute, the
>> script gives me an error repeatedly. My former Postdoc wrote this script.
>> Thus, I did not know this inside much.
>>
>> I have tried to fix it for more than a month, but now I have no idea how
>> to fix it. I would appreciate it very much if you could help and give me
>> your advice.
>>
>> Please see an attached cpp file, termed ge-r.cpp. With this cpp file and
>> other ones, I have succeeded to install a skeleton R package into R using
>> your function Rcpp.package.skeleton.
>>
>> In this ge-r.cpp, there is one R function called simulate_R() written. In
>> this R fucntion, there are two C++ functions, load() and simulate(), both
>> are described in other cpp files, called from C++ into R. With cout
>> function described in simulate_R(), I confirmed these two function work in
>> R thanks to RcppArmadillo, however, it suddenly stops with an error,
>> address(nil) cause 'unknown' in R. It has seemed to stop when it return
>> (out) at the last in ge-r.cpp. I do not know why it happens. Note that the
>> C++ script works normally after the update of the system. Only this
>> RcppArmadillo conversion from C++ function into a R function is deformed.
>>
>> Please give me an advice, please. Of course, I can give you more
>> information on the C++ script in details if you need.
>>
>> Best regards,
>>
>> Takeshi
>>
>>
>>
>> ge-r.cpp
>>
>> #ifndef __R__
>>
>> #define __R__
>> #endif
>>
>> #ifndef USE_OMP
>> #define USE_OMP
>> #endif
>>
>>
>> #include <RcppArmadillo.h>
>>
>>
>> #include "ge-model.h"
>>
>> using namespace arma;
>>
>>
>>
>> // input:
>> // parameter matrix: row for particle, col for parameter
>> // filename of observation
>> // output:
>> // simulation for regular time points: row for particle, col for time, slice for term
>> // existing observation to corresponding regular time points
>>
>> // [[Rcpp::depends(RcppArmadillo)]]
>> // [[Rcpp::export]]
>> Rcpp::List simulate_R(const arma::mat& param_r, const char* fobs, const int interval) {
>>
>> try {
>> geModel Model;
>> Model.n_thread=omp_get_num_procs();
>> Model._param=param_r;
>> cout << "params set.\n";
>>
>> cout << "filename of obs: "<< fobs << ".\n";
>>
>> Model._obs.load(fobs);
>>
>> cout << "obs loaded.\n";
>>
>> Model.n_acc=Model._param.n_rows;
>> cout << "n_acc set to be " << Model.n_acc << ".\n";
>>
>> Model._obs._out_interval = interval;
>> Model._obs._n_out_date = (Model._obs._n_date / Model._obs._out_interval) + 1;
>>
>> Model.out_y=cube(Model.n_acc, Model._obs._n_group, Model._obs._n_out_date);
>> Model.out_res_1=cube(Model.n_acc,Model._obs._n_group, Model._obs._n_out_date);
>> Model.out_res_2=cube(Model.n_acc,Model._obs._n_group, Model._obs._n_out_date);
>> Model.out_res_clock=cube(Model.n_acc,Model._obs._n_group, Model._obs._n_out_date);
>> Model.out_res_dev=cube(Model.n_acc,Model._obs._n_group, Model._obs._n_out_date);
>>
>> cout << "output matrix initialized.\n";
>>
>> //necessary for simulate_obs
>> Model._distance=vec(Model.n_acc);
>>
>> Model.simulate(0,Model.n_acc-1,true);
>> cout << "simulation complete.\n";
>>
>> fflush(stdout);
>>
>> cout << size(Model.out_y)<<".\n"<< Model.out_y[0]<<".\n"<<Model.out_y[1]<<".\n"<<Model.out_y[2]<<".\n";
>>
>> Rcpp::List out = Rcpp::List::create(
>> Rcpp::Named("out_y")=Model.out_y,
>> Rcpp::Named("out_res_1")=Model.out_res_1,
>> Rcpp::Named("out_res_2")=Model.out_res_2,
>> Rcpp::Named("out_res_clock")=Model.out_res_clock,
>> Rcpp::Named("out_res_dev")=Model.out_res_dev
>> );
>>
>> cout << "List constructed.\n";
>>
>> fflush(stdout);
>>
>> return (out);
>> }
>>
>> catch(char* e) {
>> cout << e << "\n";
>> exit(EXIT_FAILURE);
>> }
>> catch(...) {
>> cout << "Error\n";
>> exit(EXIT_FAILURE);
>> }
>> }
>>
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>
> --
> 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
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