Local package install with undefined reference error - r

Question

I am very new to the R extension with C.
The scenario is:
I want to implement the code in one package from one paper which is quite old (2007 or earlier).
I first tried to install the package with the commend
install.packages("~/ppmx_1.0.tar.gz", repos = NULL, type = "source")
Then I got errors and warnings (I am sorry it it quite long)
** libs
*** arch - i386
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bayes.c -o bayes.o
bayes.c: In function 'nn_bayes1':
bayes.c:107:5: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c cdf.c -o cdf.o
cdf.c:3:1: warning: "/*" within comment [-Wcomment]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c com.c -o com.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dcdflib.c -o dcdflib.o
dcdflib.c: In function 'cdfbin':
dcdflib.c:1889:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c: In function 'cdfgam':
dcdflib.c:3551:9: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c: In function 'E0000':
dcdflib.c:6410:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c:6434:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c:6475:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c:6342:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable]
dcdflib.c: In function 'E0001':
dcdflib.c:6877:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fortif.c -o fortif.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c interface.c -o interface.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ipmpar.c -o ipmpar.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c matrix.c -o matrix.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mess.c -o mess.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c nrutil.c -o nrutil.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ppmx.c -o ppmx.o
ppmx.c: In function 'init':
ppmx.c:69:8: warning: unused variable 'line' [-Wunused-variable]
ppmx.c:68:10: warning: unused variable 'r' [-Wunused-variable]
ppmx.c: In function 'init_config':
ppmx.c:382:13: warning: unused variable 'ct' [-Wunused-variable]
ppmx.c: In function 'gibbs':
ppmx.c:426:7: warning: unused variable 'time' [-Wunused-variable]
ppmx.c: In function 'sample_config':
ppmx.c:470:11: warning: unused variable 'j' [-Wunused-variable]
ppmx.c:470:7: warning: unused variable 'si' [-Wunused-variable]
ppmx.c: In function 'loglik':
ppmx.c:589:11: warning: unused variable 'offset' [-Wunused-variable]
ppmx.c:589:9: warning: unused variable 'k' [-Wunused-variable]
ppmx.c:589:7: warning: unused variable 'j' [-Wunused-variable]
ppmx.c: In function 'make_Sk':
ppmx.c:725:10: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
ppmx.c:724:12: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:724:9: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c: In function 'make_Sk1':
ppmx.c:742:10: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
ppmx.c:741:12: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:741:9: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c: In function 'sample_V':
ppmx.c:838:9: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:838:6: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c:837:5: warning: unused variable 'V11' [-Wunused-variable]
ppmx.c: In function 'sample_S':
ppmx.c:894:23: warning: unused variable 'S1' [-Wunused-variable]
ppmx.c:894:18: warning: unused variable 'Vinv' [-Wunused-variable]
ppmx.c:892:12: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:892:9: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c: In function 'setup_mj1':
ppmx.c:1070:20: warning: unused variable 'mu' [-Wunused-variable]
ppmx.c: In function 'setup_aj4':
ppmx.c:1147:13: warning: unused variable 'b1' [-Wunused-variable]
ppmx.c:1147:10: warning: unused variable 'a1' [-Wunused-variable]
ppmx.c: In function 'print_pars':
ppmx.c:1267:7: warning: too many arguments for format [-Wformat-extra-args]
ppmx.c: In function 'write_nclass':
ppmx.c:1401:7: warning: unused variable 'j' [-Wunused-variable]
ppmx.c:1407:1: warning: control reaches end of non-void function [-Wreturn-type]
ppmx.c: In function 'update_nclass':
ppmx.c:1396:1: warning: control reaches end of non-void function [-Wreturn-type]
ppmx.c: In function 'print_allpars':
ppmx.c:1344:1: warning: control reaches end of non-void function [-Wreturn-type]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c predict2.c -o predict2.o
predict2.c: In function 'py_update':
predict2.c:173:5: warning: unused variable 'y' [-Wunused-variable]
predict2.c:169:22: warning: unused variable 'lpr' [-Wunused-variable]
predict2.c:169:10: warning: variable 'kd' set but not used [-Wunused-but-set-variable]
predict2.c: In function 'print_pyvec':
predict2.c:343:5: warning: too many arguments for format [-Wformat-extra-args]
predict2.c: In function 'pyvec_update':
predict2.c:366:9: warning: unused variable 'sx' [-Wunused-variable]
predict2.c:364:9: warning: unused variable 'lgr' [-Wunused-variable]
predict2.c:364:5: warning: unused variable 'hC' [-Wunused-variable]
predict2.c:363:5: warning: unused variable 'r' [-Wunused-variable]
predict2.c:360:22: warning: unused variable 'lpr' [-Wunused-variable]
predict2.c:360:10: warning: variable 'kd' set but not used [-Wunused-but-set-variable]
predict2.c:358:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
predict2.c: In function 'py_update':
predict2.c:213:11: warning: 'mxh' may be used uninitialized in this function [-Wuninitialized]
predict2.c:171:5: warning: 'wmx' may be used uninitialized in this function [-Wuninitialized]
predict2.c: In function 'pyvec_update':
predict2.c:438:16: warning: 'V' may be used uninitialized in this function [-Wuninitialized]
predict2.c:438:16: warning: 'm' may be used uninitialized in this function [-Wuninitialized]
predict2.c:361:5: warning: 'wmx' may be used uninitialized in this function [-Wuninitialized]
predict2.c:427:12: warning: 'k0' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rand-nr.c -o rand-nr.o
rand-nr.c:5:1: warning: "/*" within comment [-Wcomment]
rand-nr.c:65:1: warning: "/*" within comment [-Wcomment]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rand.c -o rand.o
In file included from rand.c:60:0:
mathconst.h:23:0: warning: "M_PI" redefined [enabled by default]
c:\rtools\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:45:0: note: this is the location of the previous definition
rand.c:77:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
rand.c: In function 'pdf_norm_trunc':
rand.c:380:28: warning: variable 'lpdf' set but not used [-Wunused-but-set-variable]
rand.c:380:10: warning: unused variable 'u' [-Wunused-variable]
rand.c: In function 'cdfbeta':
rand.c:491:20: warning: variable 'x1' set but not used [-Wunused-but-set-variable]
rand.c: In function 'expdev':
rand.c:737:5: warning: variable 'b' set but not used [-Wunused-but-set-variable]
rand.c: At top level:
cdflib.h:45:13: warning: 'E0000' declared 'static' but never defined [-Wunused-function]
cdflib.h:52:13: warning: 'E0001' declared 'static' but never defined [-Wunused-function]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ranlib.c -o ranlib.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c regr.c -o regr.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c unixrep.c -o unixrep.o
In file included from unixrep.c:31:0:
mathconst.h:23:0: warning: "M_PI" redefined [enabled by default]
c:\rtools\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:45:0: note: this is the location of the previous definition
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c vector.c -o vector.o
gcc -m32 -shared -s -static-libgcc -o ppmx.dll tmp.def bayes.o cdf.o com.o dcdflib.o fortif.o interface.o ipmpar.o matrix.o mess.o nrutil.o ppmx.o predict2.o rand-nr.o rand.o ranlib.o regr.o unixrep.o vector.o -LC:/R-31~1.0/bin/i386 -lRlapack -LC:/R-31~1.0/bin/i386 -lRblas -lm -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R-31~1.0/bin/i386 -lR
fortif.o:fortif.c:(.text+0x38): undefined reference to `DPOTRF#24'
fortif.o:fortif.c:(.text+0x88): undefined reference to `DPOTRI#24'
fortif.o:fortif.c:(.text+0xf9): undefined reference to `DTRTRI#32'
fortif.o:fortif.c:(.text+0x181): undefined reference to `DSYEV#44'
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'ppmx'
* removing 'C:/R-3.1.0/library/ppmx'
Warning in install.packages :
running command '"C:/R-31~1.0/bin/x64/R" CMD INSTALL -l "C:\R-3.1.0\library" "C:/Users/kutrds11/Documents/ppmx_1.3.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/kutrds11/Documents/ppmx_1.3.tar.gz’ had non-zero exit status
I doubt the problem is the way to call .c file too old?
I know the problem is quite complicated. Is there anyone could help me please. I guess it is about the link problem bec of
fortif.o:fortif.c:(.text+0x38): undefined reference to `DPOTRF#24'
fortif.o:fortif.c:(.text+0x88): undefined reference to `DPOTRI#24'
fortif.o:fortif.c:(.text+0xf9): undefined reference to `DTRTRI#32'
fortif.o:fortif.c:(.text+0x181): undefined reference to `DSYEV#44'
I think I need toensure that my program is linked with a Lapack
library.. But I dont know how..
The fortif.c code is
static const char fortif_c_sccs_id[] = "%W%";
/*+
* fortif.c - Fortran Interface
*
* Version: %I%
*
* Description:
* Handles the interface between FORTRAN and C on the two platforms, by
* providing a single C interface to the Fortran routine, and dispatching
* according to the platform.
*
* This particular file only contains Win32 interface routines for FORTRAN
* subroutines that have a character arguments. When a FORTRAN routine is
* compiled, for each character argument in the signature the compiler
* adds another unsigned long argument immediately following it, that
* holds the length of the char array being passed to it.
*
* In Response\01, we have C routines calling FORTRAN ones, and the size
* of the char array is generally unknown (it may be passed in from the
* caller's caller). However, for the FORTRAN routines we are interested
* in, the character argument is input only, not being changed by the
* routine. Therefore, we can use the length of the string represented by
* the "char*" argument as a suitable length to pass to the FORTRAN code.
*
* Note that this ".c" file does not contain interfaces for routines that
* do not pass in character arguments; these interfaces can be handled
* by simple definitions in the associated header file.
*
* Modification History:
* 10-JUN-1999 1.1 Stephen Morris (Tessella Support Services plc)
* Created.
-*/
#include <string.h>
#define FORTIF_H_SCCS_ID
#include "fortif.h"
#if defined(_WIN32)
/*+
* dpotrf - Lapack Routine
-*/
extern void __stdcall DPOTRF(char *uplo, unsigned int uplo_length, int *n,
double *a, int *ncol_a, int *info);
void dpotrf(char *uplo, int *n, double *a, int *ncol_a, int *info)
{
DPOTRF(uplo, (unsigned int) strlen(uplo), n, a, ncol_a, info);
}
/*+
* dpotri - Lapack Routine
-*/
extern void __stdcall DPOTRI(char *uplo, unsigned int uplo_length, int *n,
double *a, int *ncol_a, int *info);
void dpotri(char *uplo, int *n, double *a, int *ncol_a, int *info)
{
DPOTRI(uplo, (unsigned int) strlen(uplo), n, a, ncol_a, info);
}
/*+
* dtrtri - Lapack Routine
-*/
extern void __stdcall DTRTRI(char *uplo, unsigned int uplo_length,
char *diag, unsigned int diag_len, int *n, double *a, int *ncol_a, int *info);
void dtrtri(char *uplo, char *diag, int *n, double *a, int *ncol_a, int *info)
{
DTRTRI(uplo, (unsigned int) strlen(uplo), diag, (unsigned int) strlen(diag),
n, a, ncol_a, info);
}
/*+
* dsyev - Lapack Routine
*/
extern void __stdcall DSYEV(char *jobz, unsigned int jobz_length,
char *uplo, unsigned int uplo_length, int *n, double *a, int *lda,
double *w, double *work, int *lwork, int *info);
void dsyev(char *jobz, char *uplo, int *n, double *a, int *lda, double *w, double *work,
int *lwork, int *info)
{
DSYEV(jobz, (unsigned int) strlen(jobz), uplo, (unsigned int) strlen(uplo),
n, a, lda, w, work, lwork, info);
}
#endif
Please help me.
I have put the link of the code below just in case:
https://www.tandfonline.com/doi/suppl/10.1198/jcgs.2011.09066?scroll=top
Please let me know if you need more specific information
Thank you so much in advance