[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 > treeMap;
multimap >::iterator it_tM;
int l =LENGTH(membership);
//Rprintf("beleptunk");
int p = 0;
map 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;jsecond.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 > bootstraps = vector
>(boots,vector(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 significantVec = vector(Nnode);
findConfCore(treeMap,bootstraps,significantVec,confnew,R);
vector > 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::iterator iter = degrees.begin();
for(multimap >::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 >::iterator it = mergers.begin(); it !=
mergers.end(); it++)
outfile << it->first+1 << ">" << it->second+1 << endl;
outfile << "*Nodes " << Nnode << endl;
k = 1;
for(multimap >::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,greater >::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+0xf
Re: [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 -- R/Finance 2012 Conference on May 11 and 12, 2012 at UIC in Chicago, IL See agenda, registration details and more at http://www.RinFinance.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check linking errors, when interfacing c++
Hi, Thanks for the suggestions. I've forgotten to point out, that R CMD COMPILE and R CMD SHLIB works fine, the dll file was indeed created. I get these undefined references when I'm trying to run R CMD INSTALL. I've read through the "Writing R extensions" and the archives, but I really don't know what am I doing wrong. More suprising, when I run the same package in windows with R CMD check, the dll for src-i386 was created, but not the 64 -bit, i'm getting: sorry, 64 bit compilation not supported (or someting similar) If anyone have an idea, comments welcome. Thanks, Zalan On 9 May 2012 14:11, Dirk Eddelbuettel wrote: > > 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 > > -- > R/Finance 2012 Conference on May 11 and 12, 2012 at UIC in Chicago, IL > See agenda, registration details and more at http://www.RinFinance.com > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check linking errors, when interfacing c++
On May 9, 2012, at 9:10 AM, Zalan Szakolci wrote: > Hi, > > Thanks for the suggestions. I've forgotten to point out, that > > R CMD COMPILE and > R CMD SHLIB > > works fine, the dll file was indeed created. I get these undefined > references when I'm trying to run R CMD INSTALL. > ... which means you are probably doing something silly in Makevars or Makefile (ideally, you should not have either) -- and that's why Dirk was asking you. > I've read through the "Writing R extensions" and the archives, but I really > don't know what am I doing wrong. > > More suprising, when I run the same package in windows with R CMD check, > the dll for src-i386 was created, but not the 64 -bit, i'm getting: sorry, > 64 bit compilation not supported (or someting similar) > You have the wrong toolchain on your PATH (see recent question here). Cheers, Simon > If anyone have an idea, comments welcome. > > Thanks, > > Zalan > > On 9 May 2012 14:11, Dirk Eddelbuettel wrote: > >> >> 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 ŒDyA‚ ... >> | ** 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 >> >> -- >> R/Finance 2012 Conference on May 11 and 12, 2012 at UIC in Chicago, IL >> See agenda, registration details and more at http://www.RinFinance.com >> > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check linking errors, when interfacing c++
Yes, you were right guys, I've deleted my Makefile from the directory, and everything goes fine. Many thanks. On 9 May 2012 15:16, Simon Urbanek wrote: > > On May 9, 2012, at 9:10 AM, Zalan Szakolci wrote: > > > Hi, > > > > Thanks for the suggestions. I've forgotten to point out, that > > > > R CMD COMPILE and > > R CMD SHLIB > > > > works fine, the dll file was indeed created. I get these undefined > > references when I'm trying to run R CMD INSTALL. > > > > ... which means you are probably doing something silly in Makevars or > Makefile (ideally, you should not have either) -- and that's why Dirk was > asking you. > > > > I've read through the "Writing R extensions" and the archives, but I > really > > don't know what am I doing wrong. > > > > More suprising, when I run the same package in windows with R CMD check, > > the dll for src-i386 was created, but not the 64 -bit, i'm getting: > sorry, > > 64 bit compilation not supported (or someting similar) > > > > You have the wrong toolchain on your PATH (see recent question here). > > Cheers, > Simon > > > > > If anyone have an idea, comments welcome. > > > > Thanks, > > > > Zalan > > > > On 9 May 2012 14:11, Dirk Eddelbuettel wrote: > > > >> > >> 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 > >> > >> -- > >> R/Finance 2012 Conference on May 11 and 12, 2012 at UIC in Chicago, IL > >> See agenda, registration details and more at http://www.RinFinance.com > >> > > > > [[alternative HTML version deleted]] > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R Installation Manual - ATLAS BLAS guidance that is not in the current version
Good afternoon. I am trying to compile a version of Rblas.dll based on ATLAS for the Corei7. I had remembered that there was mention of which file to adjust and that "xerbla" needed to be removed from one of the outputs from the last time I tried a few years ago. The most recent version of the R Installation manual does not say anything about this. An older version (2.10 I believe) has the following text: Optionally, you can install a version of ATLAS (`math-atlas.sourceforge.net' (http://math-atlas.sourceforge.net/)) tuned to your system for fast linear algebra routines. Pre-built `Rblas.dll' for various Pentium and AthlonXP chips are available in the `windows/contrib/ATLAS' area on CRAN. If you are building R from source, there are macros `USE_ATLAS' and `ATLAS_PATH' in the file `MkRules'. Set `USE_ATLAS = YES' and `ATLAS_PATH' to where the ATLAS libraries are located. You will need to make the libraries yourself(1): none of the binaries we have seen are compiled for the correct compiler. Since R has its own `xerbla' it is best to delete that in ATLAS by ar d /path/to/libf77blas.a xerbla.o Would it be possible to restore the above information to the next version of the manual for future reference, please? Thank you, Avraham Adler __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
