[Rcpp-devel] A tough RcppArmadillo Error; address(nil) cause 'unknown' in R

井澤 毅 a-izawa at mail.ecc.u-tokyo.ac.jp
Mon Jul 10 06:03:16 CEST 2017


Dear KK,

Thanks for this explanation. Now I got it.

I did not think that ge-model.cpp is involved in this problem since it 
works well as a C++ script even in our current system.

I still wonder why this ge-r.cpp works in the old system, but I will ask 
this to the maintainer of our system.

I have learned a lot from your suggestion.

Thanks again!

Best,

Takeshi


On 2017/07/10 10:34, Qiang Kou wrote:
> In line 37 of ge-model.cpp, you try to free _rand. However, if you 
> don't call initialize in line 49 first, the array won't be initialized.
>
> Best,
>
> KK
>
> On Sun, Jul 9, 2017 at 4:45 PM, 井澤 毅 <a-izawa at mail.ecc.u-tokyo.ac.jp 
> <mailto:a-izawa at mail.ecc.u-tokyo.ac.jp>> wrote:
>
>     Dear KK,
>
>     I owe you a lot! I will check it as soon as possible.
>
>     Since I am not familiar with this much, I would be very happy to
>     tell me some urls describing "initialize".
>
>     Best,
>
>     Takeshi
>
>
>     On 2017/07/10 7:38, Qiang Kou wrote:
>>     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
>>     <mailto: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 <http://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
>>>         <http://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
>>>>         <mailto:a-izawa at mail.ecc.u-tokyo.ac.jp>> wrote:
>>>>
>>>>             Dear rcpp-devel at lists.r-forge.r-project.org
>>>>             <mailto: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);
>>>>             	}
>>>>             }
>>>>
>>>>             _______________________________________________
>>>>             Rcpp-devel mailing list
>>>>             Rcpp-devel at lists.r-forge.r-project.org
>>>>             <mailto:Rcpp-devel at lists.r-forge.r-project.org>
>>>>             https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>>>             <https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel>
>>>>
>>>>
>>>>         -- 
>>>>         Qiang Kou
>>>>         qkou at umail.iu.edu <mailto:qkou at umail.iu.edu>
>>>>         School of Informatics and Computing, Indiana University
>>
>>     -- 
>>     Qiang Kou
>>     qkou at umail.iu.edu <mailto:qkou at umail.iu.edu>
>>     School of Informatics and Computing, Indiana University
>
> -- 
> Qiang Kou
> qkou at umail.iu.edu <mailto:qkou at umail.iu.edu>
> School of Informatics and Computing, Indiana University
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