Hi all, I tried to compile a script using the code below:
============================================================ Rscript compiler.R '/Users/xiaohe/WRScpp/src/test.cpp' ============================================================ And I got 7 error messages in total as shown below. I am on a Mac (OX 10.9.4), my R is 3.1.1, and I have the latest Xcode as well as the latest Rcpp and RcppArmadillo installed. A minimally reproducible script (test.cpp) is here: https://www.dropbox.com/s/dpipxzmawet0e8y/test.cpp?dl=0 And the compiler.R file I used is in this link: https://www.dropbox.com/s/4vadide49zd6hwi/compiler.R?dl=0 I would be grateful if someone could point me to the right direction regarding the causes of the errors. Thank you in advance! ============================================================ Loading required package: RcppArmadillo clang++ -I/Library/Frameworks/R.framework/Resources/include -DDEBUG -I/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -mtune=core2 -g -O0 -c /Users/xiaohe/WRScpp/src/test.cpp -o /Users/xiaohe/WRScpp/src/test.o In file included from /Users/xiaohe/WRScpp/src/test.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo:131: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/blas_bones.hpp:62:10: error: conflicting types for 'ddot_' double arma_fortran(arma_ddot)(blas_int* n, const double* x, blas_int* incx, const double* y, blas_int* incy); ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:36:34: note: expanded from macro 'arma_fortran' #define arma_fortran(function) arma_fortran2_noprefix(function) ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:25:44: note: expanded from macro 'arma_fortran2_noprefix' #define arma_fortran2_noprefix(function) function##_ ^ <scratch space>:539:1: note: expanded from here ddot_ ^ /Library/Frameworks/R.framework/Resources/include/R_ext/BLAS.h:58:1: note: previous declaration is here F77_NAME(ddot)(const int *n, const double *dx, const int *incx, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:86:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:181:1: note: expanded from here ddot_ ^ In file included from /Users/xiaohe/WRScpp/src/test.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo:131: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/blas_bones.hpp:67:8: error: conflicting types for 'zgemv_' void arma_fortran(arma_zgemv)(const char* transA, const blas_int* m, const blas_int* n, const void* alpha, const void* A, const blas_int* ldA, const void* x, const blas_int* incx, con... ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:36:34: note: expanded from macro 'arma_fortran' #define arma_fortran(function) arma_fortran2_noprefix(function) ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:25:44: note: expanded from macro 'arma_fortran2_noprefix' #define arma_fortran2_noprefix(function) function##_ ^ <scratch space>:539:1: note: expanded from here zgemv_ ^ /Library/Frameworks/R.framework/Resources/include/R_ext/BLAS.h:287:5: note: previous declaration is here F77_NAME(zgemv)(char *trans, int *m, int *n, Rcomplex *alpha, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:86:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:3:1: note: expanded from here zgemv_ ^ In file included from /Users/xiaohe/WRScpp/src/test.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo:131: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/blas_bones.hpp:72:8: error: conflicting types for 'zgemm_' void arma_fortran(arma_zgemm)(const char* transA, const char* transB, const blas_int* m, const blas_int* n, const blas_int* k, const void* alpha, const void* A, const blas_int* ldA, con... ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:36:34: note: expanded from macro 'arma_fortran' #define arma_fortran(function) arma_fortran2_noprefix(function) ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:25:44: note: expanded from macro 'arma_fortran2_noprefix' #define arma_fortran2_noprefix(function) function##_ ^ <scratch space>:539:1: note: expanded from here zgemm_ ^ /Library/Frameworks/R.framework/Resources/include/R_ext/BLAS.h:281:5: note: previous declaration is here F77_NAME(zgemm)(const char *transa, const char *transb, const int *m, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:86:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:2:1: note: expanded from here zgemm_ ^ In file included from /Users/xiaohe/WRScpp/src/test.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo:131: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/blas_bones.hpp:78:8: error: conflicting types for 'zherk_' void arma_fortran(arma_zherk)(const char* uplo, const char* transA, const blas_int* n, const blas_int* k, const double* alpha, const void* A, const blas_int* ldA, const double* beta, vo... ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:36:34: note: expanded from macro 'arma_fortran' #define arma_fortran(function) arma_fortran2_noprefix(function) ^ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:25:44: note: expanded from macro 'arma_fortran2_noprefix' #define arma_fortran2_noprefix(function) function##_ ^ <scratch space>:539:1: note: expanded from here zherk_ ^ /Library/Frameworks/R.framework/Resources/include/R_ext/BLAS.h:319:5: note: previous declaration is here F77_NAME(zherk)(char *uplo, char *trans, int *n, int *k, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:86:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:12:1: note: expanded from here zherk_ ^ In file included from /Users/xiaohe/WRScpp/src/test.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo:137: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/blas_wrapper.hpp:46:7: error: no matching function for call to 'zgemv_' arma_fortran(arma_zgemv)(transA, m, n, (const T*)alpha, (const T*)A, ldA, (const T*)x, incx, (const T*)beta, (T*)y, incy); ^~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:36:34: note: expanded from macro 'arma_fortran' #define arma_fortran(function) arma_fortran2_noprefix(function) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:25:44: note: expanded from macro 'arma_fortran2_noprefix' #define arma_fortran2_noprefix(function) function##_ ^~~~~~~~~~~ <scratch space>:25:1: note: expanded from here zgemv_ ^~~~~~ /Library/Frameworks/R.framework/Resources/include/R_ext/BLAS.h:287:5: note: candidate function not viable: 1st argument ('const char *') would lose const qualifier F77_NAME(zgemv)(char *trans, int *m, int *n, Rcomplex *alpha, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:86:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:3:1: note: expanded from here zgemv_ ^ In file included from /Users/xiaohe/WRScpp/src/test.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo:137: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/blas_wrapper.hpp:81:7: error: no matching function for call to 'zgemm_' arma_fortran(arma_zgemm)(transA, transB, m, n, k, (const T*)alpha, (const T*)A, ldA, (const T*)B, ldB, (const T*)beta, (T*)C, ldC); ^~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:36:34: note: expanded from macro 'arma_fortran' #define arma_fortran(function) arma_fortran2_noprefix(function) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:25:44: note: expanded from macro 'arma_fortran2_noprefix' #define arma_fortran2_noprefix(function) function##_ ^~~~~~~~~~~ <scratch space>:25:1: note: expanded from here zgemm_ ^~~~~~ /Library/Frameworks/R.framework/Resources/include/R_ext/BLAS.h:281:5: note: candidate function not viable: no known conversion from 'const T *' (aka 'const complex<double> *') to 'const Rcomplex *' for 6th argument F77_NAME(zgemm)(const char *transa, const char *transb, const int *m, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:86:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:2:1: note: expanded from here zgemm_ ^ In file included from /Users/xiaohe/WRScpp/src/test.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo:137: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/blas_wrapper.hpp:130:7: error: no matching function for call to 'zherk_' arma_fortran(arma_zherk)(uplo, transA, n, k, (const TT*)alpha, (const cx_TT*)A, ldA, (const TT*)beta, (cx_TT*)C, ldC); ^~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:36:34: note: expanded from macro 'arma_fortran' #define arma_fortran(function) arma_fortran2_noprefix(function) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:25:44: note: expanded from macro 'arma_fortran2_noprefix' #define arma_fortran2_noprefix(function) function##_ ^~~~~~~~~~~ <scratch space>:25:1: note: expanded from here zherk_ ^~~~~~ /Library/Frameworks/R.framework/Resources/include/R_ext/BLAS.h:319:5: note: candidate function not viable: 1st argument ('const char *') would lose const qualifier F77_NAME(zherk)(char *uplo, char *trans, int *n, int *k, ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:86:24: note: expanded from macro 'F77_NAME' #define F77_NAME(x) F77_CALL(x) ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:12:1: note: expanded from here zherk_ ^ 7 errors generated. make: *** [/Users/xiaohe/WRScpp/src/test.o] Error 1 ============================================================ Best, Xiao
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