Zalan Szakolci
2012-May-08 22:35 UTC
[Rd] R CMD check linking errors, when interfacing c++
Hi there,
I am trying to interface c++ code in R and make a package. With R CMD SHLIB
the dll was created, but when I try R CMD check, I am getting 'undefined
reference to..' linkage error messages.
The relevant c++ source from conf-infomap.cpp:
#include "conf-infomap.h"
#include "R.h" // R functions
#include "Rinternals.h"
#include "Rmath.h" // R math
#include "Rdefines.h"
using namespace std;
using std::cout;
using std::cin;
using std::endl;
[...]
extern "C" {
void RosvallDynamicSkeleton(int *seed,char** file, int *attempts, int
*resamples, double *conf) {
int ret = confInfomap(seed[0],file,attempts[0],resamples[0],conf[0]);
if(ret == 0)
Rprintf("cluster map has been written to %s\n", file[0]);
R_FlushConsole();
R_ProcessEvents();
return; // Return Nothing.
}
}
extern "C" {
void findConfCoreWrapper(SEXP gdiag, SEXP bootClusters, SEXP membership,
SEXP conf) {
multimap<double,treeNode,greater<double> > treeMap;
multimap<double,treeNode,greater<double> >::iterator it_tM;
int l =LENGTH(membership);
//Rprintf("beleptunk");
int p = 0;
map<int,int> degrees;
for(int i=0;i < l;i++){
SEXP members = VECTOR_ELT(membership,i);
//Rprintf("%d\n",Nmembers);
SEXP membersSXP = VECTOR_ELT(members,0);
SEXP sizesxp = VECTOR_ELT(members,1);
double* sizevc = REAL(sizesxp);
double size = sizevc[0];
int Nmembers = LENGTH(membersSXP);
treeNode tmp_tN;
//Rprintf("the size of the module is: %f\n",size);
it_tM = treeMap.insert(make_pair(size,tmp_tN));
//Rprintf("%d\n",Nmembers);
for(int j=0;j<Nmembers;j++)
{
SEXP node = VECTOR_ELT(membersSXP,j);
SEXP nodesizesxp = VECTOR_ELT(node,0);
SEXP nodeidsxp = VECTOR_ELT(node,1);
SEXP nodenamesxp = VECTOR_ELT(node,2);
int degree = INTEGER(VECTOR_ELT(node,3))[0];
int nodeid = INTEGER(nodeidsxp)[0];
degrees.insert(make_pair(nodeid,degree));
string nodename = string(CHAR(STRING_ELT(nodenamesxp,0)));
double nodesize = REAL(nodesizesxp)[0];
//Rprintf("nodename:%s",nodename.c_str());
it_tM->second.members.insert(make_pair(nodesize,make_pair(nodeid,nodename)));
//Rprintf("the node is: %s\n",nodename.c_str());
//Rprintf("the size of the node is: %f\n",nodesize);
//Rprintf("the id of the node is: %d\n",nodeid);
}
p = i;
}
//return;
int boots = LENGTH(bootClusters);
SEXP memberssxp = VECTOR_ELT(bootClusters,0);
int ltemp = LENGTH(memberssxp);
vector<vector<int > > bootstraps = vector<vector<int
>>(boots,vector<int>(ltemp));
for(int i =0 ; i< boots;++i)
{
SEXP memberssxp = VECTOR_ELT(bootClusters,i);
int l = LENGTH(memberssxp);
int* members = INTEGER(memberssxp);
//bootstraps[i] = new int[l];
for(int j = 0; j<l;++j)
{
bootstraps[i][j] = members[j];
//Rprintf("id: %d\n",members[j]);
}
}
double confnew = REAL(conf)[0];
int Nnode = LENGTH(VECTOR_ELT(bootClusters,0));
MTRand *R = new MTRand(long(443)); // Set random seed
vector<bool> significantVec = vector<bool>(Nnode);
findConfCore(treeMap,bootstraps,significantVec,confnew,R);
vector<pair<int,int> > mergers;
findConfModules(treeMap,bootstraps,significantVec,mergers,confnew);
SEXP name = VECTOR_ELT(gdiag,0);
SEXP links = VECTOR_ELT(gdiag,2);
Rprintf("teve");
int totalDegree = INTEGER(VECTOR_ELT(gdiag,4))[0]*2;
string networkName = string(CHAR(STRING_ELT(name,0)));
ofstream outfile;
ostringstream oss;
int nLinks = INTEGER(links)[0];
oss.str("");
oss << networkName << ".smap";
outfile.open(oss.str().c_str());
outfile << "# modules: " << l << endl;
outfile << "# modulelinks: " << "na" <<
endl;
outfile << "# nodes: " << Nnode << endl;
outfile << "# links: " << nLinks << endl;
outfile << "# codelength: " << "na" <<
endl;
outfile << "*Undirected" << endl;
outfile << "*Modules " << l << endl;
int k = 0;
map<int,int>::iterator iter = degrees.begin();
for(multimap<double,treeNode,greater<double> >::iterator it
treeMap.begin(); it != treeMap.end(); it++){
outfile << k+1 << " \"" <<
it->second.members.begin()->second.second <<
",...\" " << it->first << " " <<
(double)iter->second
/(double)totalDegree<< endl;
p++;
k++;
}
outfile << "*Insignificants " << mergers.size() <<
endl;
for(vector<pair<int,int> >::iterator it = mergers.begin(); it
!mergers.end(); it++)
outfile << it->first+1 << ">" <<
it->second+1 << endl;
outfile << "*Nodes " << Nnode << endl;
k = 1;
for(multimap<double,treeNode,greater<double> >::iterator it
treeMap.begin(); it != treeMap.end(); it++){
string s;
s.append(to_string(k));
printSignificantTree(s,it,&outfile,significantVec);
k++;
}
outfile << "*Links " << nLinks << endl;
/*
for(multimap<double,pair<int,int>,greater<double>
>::iterator it sortedLinks.begin();it != sortedLinks.end();it++)
outfile << it->second.first << " " <<
it->second.second << " " <<
1.0*it->first << endl;
*/
outfile.close();
delete R;
Rprintf("done");
R_FlushConsole();
R_ProcessEvents();
return; // Return Nothing.
}
}
Now when I run R CMD check, in file 00install.out I am getting the
following linking errors:
* installing *source* package ‘DyA’ ...
** libs
** arch -
g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
-pipe -c conf-infomap.cpp -o conf-infomap.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
-pipe -c GreedyBase.cpp -o GreedyBase.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
-pipe -c Greedy.cpp -o Greedy.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
-pipe -c Node.cc -o Node.o
g++ conf-infomap.o GreedyBase.o Greedy.o Node.o mersenne.cpp stoc1.cpp
userintf.cpp -lm -o conf-infomap
/usr/lib/gcc/x86_64-linux-gnu/4.6.1/../../../x86_64-linux-gnu/crt1.o: In
function `_start':
(.text+0x20): undefined reference to `main'
conf-infomap.o: In function `findConfCoreWrapper':
conf-infomap.cpp:(.text+0xfd47): undefined reference to `LENGTH'
conf-infomap.cpp:(.text+0xfdc2): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0xfdcf): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0xfde1): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0xfde9): undefined reference to `REAL'
conf-infomap.cpp:(.text+0xfdf6): undefined reference to `LENGTH'
conf-infomap.cpp:(.text+0xffc9): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0xffd6): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0xffe6): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0xfff6): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x10006): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x1000e): undefined reference to `INTEGER'
conf-infomap.cpp:(.text+0x1001c): undefined reference to `INTEGER'
conf-infomap.cpp:(.text+0x10071): undefined reference to `STRING_ELT'
conf-infomap.cpp:(.text+0x10079): undefined reference to `R_CHAR'
conf-infomap.cpp:(.text+0x10099): undefined reference to `REAL'
conf-infomap.cpp:(.text+0x1022d): undefined reference to `LENGTH'
conf-infomap.cpp:(.text+0x1023c): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x10244): undefined reference to `LENGTH'
conf-infomap.cpp:(.text+0x10638): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x10643): undefined reference to `LENGTH'
conf-infomap.cpp:(.text+0x1064e): undefined reference to `INTEGER'
conf-infomap.cpp:(.text+0x10776): undefined reference to `REAL'
conf-infomap.cpp:(.text+0x1078b): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x10793): undefined reference to `LENGTH'
conf-infomap.cpp:(.text+0x10aba): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x10acc): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x10add): undefined reference to `Rprintf'
conf-infomap.cpp:(.text+0x10aec): undefined reference to `VECTOR_ELT'
conf-infomap.cpp:(.text+0x10af4): undefined reference to `INTEGER'
conf-infomap.cpp:(.text+0x10b03): undefined reference to `STRING_ELT'
conf-infomap.cpp:(.text+0x10b0b): undefined reference to `R_CHAR'
conf-infomap.cpp:(.text+0x10c17): undefined reference to `INTEGER'
conf-infomap.cpp:(.text+0x11123): undefined reference to `Rprintf'
conf-infomap.cpp:(.text+0x11128): undefined reference to `R_FlushConsole'
conf-infomap.cpp:(.text+0x1112d): undefined reference to `R_ProcessEvents'
conf-infomap.o: In function `RosvallDynamicSkeleton':
conf-infomap.cpp:(.text+0x15133): undefined reference to `Rprintf'
conf-infomap.cpp:(.text+0x15138): undefined reference to `R_FlushConsole'
conf-infomap.cpp:(.text+0x1513e): undefined reference to `R_ProcessEvents'
collect2: ld returned 1 exit status
make: *** [conf-infomap] Error 1
Can anyone help, what am I doing wrong?
I am using R 2.15.0 on ubuntu 11.10
Many thanks,
Zalan
[[alternative HTML version deleted]]
Dirk Eddelbuettel
2012-May-09 12:11 UTC
[Rd] R CMD check linking errors, when interfacing c++
On 9 May 2012 at 00:35, Zalan Szakolci wrote:
| Hi there,
|
| I am trying to interface c++ code in R and make a package. With R CMD SHLIB
| the dll was created, but when I try R CMD check, I am getting 'undefined
| reference to..' linkage error messages.
|
| The relevant c++ source from conf-infomap.cpp:
[...]
| Now when I run R CMD check, in file 00install.out I am getting the
| following linking errors:
|
| * installing *source* package ?DyA? ...
| ** libs
| ** arch -
| g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
| -pipe -c conf-infomap.cpp -o conf-infomap.o
| g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
| -pipe -c GreedyBase.cpp -o GreedyBase.o
| g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
| -pipe -c Greedy.cpp -o Greedy.o
| g++ -I/usr/share/R/include -DNDEBUG -fpic -I -Wall -O3 -funroll-loops
| -pipe -c Node.cc -o Node.o
| g++ conf-infomap.o GreedyBase.o Greedy.o Node.o mersenne.cpp stoc1.cpp
| userintf.cpp -lm -o conf-infomap
What is your src/Makevars file?
This looks very wrong as you are obviously not linking against R itself.
I would recommend a good long look at both the 'Writing R Extensions'
manual
as well as some of the existing CRAN packages uses C++ sources.
You can (and should) also try
R CMD COMPILE ...
R CMD SHLIB ...
R CMD INSTALL ...
etc as 'R CMD check' is really only the final bit.
Dirk
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