* installing *source* package ‘BRISC’ ... ** package ‘BRISC’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++-13 -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E checking for g++-13 -std=gnu++17 option to support OpenMP... -fopenmp configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noRemap/BRISC/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c BRISC.cpp -o BRISC.o BRISC.cpp: In function 'double updateBF(double*, double*, double*, double*, double*, double*, int*, int*, int, double*, int, int, double)': BRISC.cpp:99:116: error: 'error' was not declared in this scope; did you mean 'perror'? 99 | F77_NAME(dpotrf)(&lower, &nnIndxLU[n+i], &C[CIndx[i]], &nnIndxLU[n+i], &info FCONE); if(info != 0){error("c++ error: dpotrf failed\n");} | ^~~~~ | perror BRISC.cpp:100:116: error: 'error' was not declared in this scope; did you mean 'perror'? 100 | F77_NAME(dpotri)(&lower, &nnIndxLU[n+i], &C[CIndx[i]], &nnIndxLU[n+i], &info FCONE); if(info != 0){error("c++ error: dpotri failed\n");} | ^~~~~ | perror BRISC.cpp: In function 'double processed_output(double*, double*, double*, double*, int*, int*, int*, int, int, int, double*, int, int, int, double, double*, double*, double*, double*, double*, double*, double)': BRISC.cpp:177:77: error: 'error' was not declared in this scope; did you mean 'perror'? 177 | F77_NAME(dpotrf)(lower, &p, tmp_pp, &p, &info FCONE); if(info != 0){error("c++ error: dpotrf failed\n");} | ^~~~~ | perror BRISC.cpp:178:77: error: 'error' was not declared in this scope; did you mean 'perror'? 178 | F77_NAME(dpotri)(lower, &p, tmp_pp, &p, &info FCONE); if(info != 0){error("c++ error: dpotri failed\n");} | ^~~~~ | perror BRISC.cpp: In function 'double likelihood(double*, double*, double*, double*, int*, int*, int*, int, int, int, double*, int, int, int, double)': BRISC.cpp:258:77: error: 'error' was not declared in this scope; did you mean 'perror'? 258 | F77_NAME(dpotrf)(lower, &p, tmp_pp, &p, &info FCONE); if(info != 0){error("c++ error: dpotrf failed\n");} | ^~~~~ | perror BRISC.cpp:259:77: error: 'error' was not declared in this scope; did you mean 'perror'? 259 | F77_NAME(dpotri)(lower, &p, tmp_pp, &p, &info FCONE); if(info != 0){error("c++ error: dpotri failed\n");} | ^~~~~ | perror BRISC.cpp: In function 'void processed_bootstrap_output(double*, double*, double*, double*, int*, int*, int*, int, int, int, double*, int, int, int, double, double*, double*, double)': BRISC.cpp:362:77: error: 'error' was not declared in this scope; did you mean 'perror'? 362 | F77_NAME(dpotrf)(lower, &p, tmp_pp, &p, &info FCONE); if(info != 0){error("c++ error: dpotrf failed\n");} | ^~~~~ | perror BRISC.cpp:363:77: error: 'error' was not declared in this scope; did you mean 'perror'? 363 | F77_NAME(dpotri)(lower, &p, tmp_pp, &p, &info FCONE); if(info != 0){error("c++ error: dpotri failed\n");} | ^~~~~ | perror In file included from BRISC.cpp:14: BRISC.cpp: In function 'SEXPREC* process_bootstrap_data(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': BRISC.cpp:409:57: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 409 | SEXP residual_boot_r; PROTECT(residual_boot_r = allocVector(REALSXP, n_nngp)); nProtect++; double *residual_boot = REAL(residual_boot_r); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ BRISC.cpp:423:41: error: 'mkChar' was not declared in this scope 423 | SET_VECTOR_ELT(resultName_r, 0, mkChar("result")); | ^~~~~~ BRISC.cpp:426:9: error: 'namesgets' was not declared in this scope; did you mean 'Rf_namesgets'? 426 | namesgets(result_r, resultName_r); | ^~~~~~~~~ | Rf_namesgets BRISC.cpp: In function 'SEXPREC* BRISC_bootstrapcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': BRISC.cpp:458:57: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 458 | SEXP residual_boot_r; PROTECT(residual_boot_r = allocVector(REALSXP, n_nngp)); nProtect++; double *residual_boot = REAL(residual_boot_r); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ BRISC.cpp:522:41: error: 'mkChar' was not declared in this scope 522 | SET_VECTOR_ELT(resultName_r, 0, mkChar("theta")); | ^~~~~~ BRISC.cpp:527:9: error: 'namesgets' was not declared in this scope; did you mean 'Rf_namesgets'? 527 | namesgets(result_r, resultName_r); | ^~~~~~~~~ | Rf_namesgets BRISC.cpp: In function 'SEXPREC* BRISC_estimatecpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': BRISC.cpp:604:43: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 604 | SEXP nnIndx_r; PROTECT(nnIndx_r = allocVector(INTSXP, nIndx)); nProtect++; nnIndx_nngp = INTEGER(nnIndx_r); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ BRISC.cpp:732:41: error: 'mkChar' was not declared in this scope 732 | SET_VECTOR_ELT(resultName_r, 0, mkChar("B")); | ^~~~~~ BRISC.cpp:774:9: error: 'namesgets' was not declared in this scope; did you mean 'Rf_namesgets'? 774 | namesgets(result_r, resultName_r); | ^~~~~~~~~ | Rf_namesgets BRISC.cpp: In function 'SEXPREC* BRISC_correlationcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': BRISC.cpp:889:45: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 889 | SEXP sim_cor_r; PROTECT(sim_cor_r = allocVector(REALSXP, tot_length)); nProtect++; double *sim_cor = REAL(sim_cor_r); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ BRISC.cpp:930:41: error: 'mkChar' was not declared in this scope 930 | SET_VECTOR_ELT(resultName_r, 0, mkChar("norm_sim")); | ^~~~~~ BRISC.cpp:935:9: error: 'namesgets' was not declared in this scope; did you mean 'Rf_namesgets'? 935 | namesgets(result_r, resultName_r); | ^~~~~~~~~ | Rf_namesgets BRISC.cpp:914:16: warning: unused variable 'logDet' [-Wunused-variable] 914 | double logDet = updateBF(B, F, c, C, D, d, nnIndxLU, CIndx, n, theta, covModel, nThreads, fix_nugget); | ^~~~~~ BRISC.cpp: In function 'SEXPREC* BRISC_decorrelationcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': BRISC.cpp:1052:49: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 1052 | SEXP sim_decor_r; PROTECT(sim_decor_r = allocVector(REALSXP, tot_length)); nProtect++; double *sim_decor = REAL(sim_decor_r); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ BRISC.cpp:1092:41: error: 'mkChar' was not declared in this scope 1092 | SET_VECTOR_ELT(resultName_r, 0, mkChar("sim")); | ^~~~~~ BRISC.cpp:1097:9: error: 'namesgets' was not declared in this scope; did you mean 'Rf_namesgets'? 1097 | namesgets(result_r, resultName_r); | ^~~~~~~~~ | Rf_namesgets BRISC.cpp:1076:16: warning: unused variable 'logDet' [-Wunused-variable] 1076 | double logDet = updateBF(B, F, c, C, D, d, nnIndxLU, CIndx, n, theta, covModel, nThreads, fix_nugget); | ^~~~~~ BRISC.cpp: In function 'SEXPREC* BRISC_neighborcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': BRISC.cpp:1148:43: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 1148 | SEXP nnIndx_r; PROTECT(nnIndx_r = allocVector(INTSXP, nIndx)); nProtect++; nnIndx_nngp = INTEGER(nnIndx_r); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ BRISC.cpp:1207:41: error: 'mkChar' was not declared in this scope 1207 | SET_VECTOR_ELT(resultName_r, 0, mkChar("nnIndxLU")); | ^~~~~~ BRISC.cpp:1225:9: error: 'namesgets' was not declared in this scope; did you mean 'Rf_namesgets'? 1225 | namesgets(result_r, resultName_r); | ^~~~~~~~~ | Rf_namesgets BRISC.cpp: In function 'SEXPREC* BRISC_estimateneighborcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': BRISC.cpp:1313:37: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 1313 | SEXP llk_r; PROTECT(llk_r = allocVector(REALSXP, 1)); nProtect++; double* llk_nngp = REAL(llk_r); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ BRISC.cpp:1393:41: error: 'mkChar' was not declared in this scope 1393 | SET_VECTOR_ELT(resultName_r, 0, mkChar("B")); | ^~~~~~ BRISC.cpp:1416:9: error: 'namesgets' was not declared in this scope; did you mean 'Rf_namesgets'? 1416 | namesgets(result_r, resultName_r); | ^~~~~~~~~ | Rf_namesgets BRISC.cpp:1238:13: warning: unused variable 'i' [-Wunused-variable] 1238 | int i, k, l, nProtect=0; | ^ BRISC.cpp:1238:16: warning: unused variable 'k' [-Wunused-variable] 1238 | int i, k, l, nProtect=0; | ^ BRISC.cpp:1238:19: warning: unused variable 'l' [-Wunused-variable] 1238 | int i, k, l, nProtect=0; | ^ BRISC.cpp:1248:17: warning: unused variable 'coords' [-Wunused-variable] 1248 | double *coords = REAL(coords_r); | ^~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: BRISC.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/BRISC/src' ERROR: compilation failed for package ‘BRISC’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/BRISC-lib/BRISC’ Command exited with non-zero status 1 Time 0:08.62, 3.38 + 1.60