* installing *source* package ‘MDFS’ ... ** package ‘MDFS’ successfully unpacked and MD5 sums checked ** using staged installation MDFS: Running configure ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ using C++17 make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noRemap/MDFS/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -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 cpu/discretize.cpp -o cpu/discretize.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -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 cpu/common.cpp -o cpu/common.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -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 r_init.cpp -o r_init.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -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 r_interface.cpp -o r_interface.o r_interface.cpp: In function 'SEXPREC* r_compute_max_ig(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': r_interface.cpp:29:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 29 | if (asLogical(Rin_use_cuda)) { | ^~~~~~~~~ | Rf_asLogical r_interface.cpp:30:9: error: 'error' was not declared in this scope; did you mean 'perror'? 30 | error("CUDA acceleration not compiled"); | ^~~~~ | perror r_interface.cpp:34:35: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 34 | const int* dataDims = INTEGER(getAttrib(Rin_data, R_DimSymbol)); | ^~~~~~~~~ | Rf_getAttrib r_interface.cpp:36:10: error: 'isNull' was not declared in this scope 36 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:43:10: error: 'isNull' was not declared in this scope 43 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:83:33: error: 'asInteger' was not declared in this scope; did you mean 'Rf_asInteger'? 83 | const int discretizations = asInteger(Rin_discretizations); | ^~~~~~~~~ | Rf_asInteger r_interface.cpp:90:10: error: 'isNull' was not declared in this scope 90 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:98:9: error: 'asReal' was not declared in this scope 98 | asReal(Rin_range) | ^~~~~~ r_interface.cpp:108:9: error: 'length' was not declared in this scope 108 | length(Rin_interesting_vars), | ^~~~~~ r_interface.cpp:109:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 109 | asLogical(Rin_require_all_vars), | ^~~~~~~~~ | Rf_asLogical In file included from r_interface.h:1, from r_interface.cpp:4: r_interface.cpp:114:33: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 114 | SEXP Rout_max_igs = PROTECT(allocVector(REALSXP, variable_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:119:10: error: 'isNull' was not declared in this scope 119 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:126:31: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 126 | Rout_tuples = PROTECT(allocMatrix(INTSXP, mdfs_info.dimensions, variable_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:142:10: error: 'isNull' was not declared in this scope 142 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:155:10: error: 'isNull' was not declared in this scope 155 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:165:10: error: 'isNull' was not declared in this scope 165 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp: In function 'SEXPREC* r_compute_max_ig_discrete(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': r_interface.cpp:186:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 186 | if (asLogical(Rin_use_cuda)) { | ^~~~~~~~~ | Rf_asLogical r_interface.cpp:187:9: error: 'error' was not declared in this scope; did you mean 'perror'? 187 | error("CUDA acceleration not compiled"); | ^~~~~ | perror r_interface.cpp:191:35: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 191 | const int* dataDims = INTEGER(getAttrib(Rin_data, R_DimSymbol)); | ^~~~~~~~~ | Rf_getAttrib r_interface.cpp:193:10: error: 'isNull' was not declared in this scope 193 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:200:10: error: 'isNull' was not declared in this scope 200 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:210:27: error: 'asInteger' was not declared in this scope; did you mean 'Rf_asInteger'? 210 | const int divisions = asInteger(Rin_divisions); | ^~~~~~~~~ | Rf_asInteger r_interface.cpp:216:10: error: 'isNull' was not declared in this scope 216 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:224:9: error: 'asReal' was not declared in this scope 224 | asReal(Rin_pseudocount), | ^~~~~~ r_interface.cpp:227:9: error: 'length' was not declared in this scope 227 | length(Rin_interesting_vars), | ^~~~~~ r_interface.cpp:228:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 228 | asLogical(Rin_require_all_vars), | ^~~~~~~~~ | Rf_asLogical r_interface.cpp:233:33: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 233 | SEXP Rout_max_igs = PROTECT(allocVector(REALSXP, variable_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:238:10: error: 'isNull' was not declared in this scope 238 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:245:31: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 245 | Rout_tuples = PROTECT(allocMatrix(INTSXP, mdfs_info.dimensions, variable_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:261:10: error: 'isNull' was not declared in this scope 261 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:274:10: error: 'isNull' was not declared in this scope 274 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp:284:10: error: 'isNull' was not declared in this scope 284 | if (!isNull(Rin_contrast_data)) { | ^~~~~~ r_interface.cpp: In function 'SEXPREC* r_compute_all_matching_tuples(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': r_interface.cpp:309:35: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 309 | const int* dataDims = INTEGER(getAttrib(Rin_data, R_DimSymbol)); | ^~~~~~~~~ | Rf_getAttrib r_interface.cpp:314:33: error: 'asInteger' was not declared in this scope; did you mean 'Rf_asInteger'? 314 | const int discretizations = asInteger(Rin_discretizations); | ^~~~~~~~~ | Rf_asInteger r_interface.cpp:318:10: error: 'isNull' was not declared in this scope 318 | if (!isNull(Rin_decision)) { | ^~~~~~ r_interface.cpp:328:9: error: 'asReal' was not declared in this scope 328 | asReal(Rin_range) | ^~~~~~ r_interface.cpp:332:10: error: 'isNull' was not declared in this scope 332 | if (!isNull(Rin_I_lower)) { | ^~~~~~ r_interface.cpp:343:9: error: 'length' was not declared in this scope 343 | length(Rin_interesting_vars), | ^~~~~~ r_interface.cpp:344:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 344 | asLogical(Rin_require_all_vars), | ^~~~~~~~~ | Rf_asLogical r_interface.cpp:352:9: error: 'isNull' was not declared in this scope 352 | if (isNull(Rin_decision)) { | ^~~~~~ r_interface.cpp:360:22: error: 'error' was not declared in this scope; did you mean 'perror'? 360 | default: error("Unknown statistic"); | ^~~~~ | perror r_interface.cpp:370:22: error: 'error' was not declared in this scope; did you mean 'perror'? 370 | default: error("Unknown statistic"); | ^~~~~ | perror r_interface.cpp:375:36: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 375 | SEXP Rout_result = PROTECT(allocMatrix(REALSXP, variable_count, variable_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:388:33: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 388 | SEXP Rout_igs = PROTECT(allocVector(REALSXP, tuples_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:389:36: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 389 | SEXP Rout_tuples = PROTECT(allocMatrix(INTSXP, tuples_count, mdfs_info.dimensions)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp: In function 'SEXPREC* r_compute_all_matching_tuples_discrete(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': r_interface.cpp:423:35: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 423 | const int* dataDims = INTEGER(getAttrib(Rin_data, R_DimSymbol)); | ^~~~~~~~~ | Rf_getAttrib r_interface.cpp:428:27: error: 'asInteger' was not declared in this scope; did you mean 'Rf_asInteger'? 428 | const int divisions = asInteger(Rin_divisions); | ^~~~~~~~~ | Rf_asInteger r_interface.cpp:431:10: error: 'isNull' was not declared in this scope 431 | if (!isNull(Rin_decision)) { | ^~~~~~ r_interface.cpp:438:10: error: 'isNull' was not declared in this scope 438 | if (!isNull(Rin_I_lower)) { | ^~~~~~ r_interface.cpp:446:9: error: 'asReal' was not declared in this scope 446 | asReal(Rin_pseudocount), | ^~~~~~ r_interface.cpp:449:9: error: 'length' was not declared in this scope 449 | length(Rin_interesting_vars), | ^~~~~~ r_interface.cpp:450:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 450 | asLogical(Rin_require_all_vars), | ^~~~~~~~~ | Rf_asLogical r_interface.cpp:458:9: error: 'isNull' was not declared in this scope 458 | if (isNull(Rin_decision)) { | ^~~~~~ r_interface.cpp:466:22: error: 'error' was not declared in this scope; did you mean 'perror'? 466 | default: error("Unknown statistic"); | ^~~~~ | perror r_interface.cpp:476:22: error: 'error' was not declared in this scope; did you mean 'perror'? 476 | default: error("Unknown statistic"); | ^~~~~ | perror r_interface.cpp:481:36: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 481 | SEXP Rout_result = PROTECT(allocMatrix(REALSXP, variable_count, variable_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:494:33: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 494 | SEXP Rout_igs = PROTECT(allocVector(REALSXP, tuples_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp:495:36: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 495 | SEXP Rout_tuples = PROTECT(allocMatrix(INTSXP, tuples_count, mdfs_info.dimensions)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp: In function 'SEXPREC* r_discretize(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': r_interface.cpp:524:31: error: 'length' was not declared in this scope 524 | const R_len_t obj_count = length(Rin_variable); | ^~~~~~ r_interface.cpp:525:35: error: 'asInteger' was not declared in this scope; did you mean 'Rf_asInteger'? 525 | const int discretization_nr = asInteger(Rin_discretization_nr); | ^~~~~~~~~ | Rf_asInteger r_interface.cpp:529:20: error: 'asReal' was not declared in this scope 529 | double range = asReal(Rin_range); | ^~~~~~ r_interface.cpp:537:32: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 537 | SEXP Rout_result = PROTECT(allocVector(INTSXP, obj_count)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ r_interface.cpp: In function 'SEXPREC* r_omp_set_num_threads(SEXP)': r_interface.cpp:550:29: error: 'asInteger' was not declared in this scope; did you mean 'Rf_asInteger'? 550 | const int num_threads = asInteger(Rin_num_threads); | ^~~~~~~~~ | Rf_asInteger r_interface.cpp: In function 'SEXPREC* r_compute_all_matching_tuples(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': r_interface.cpp:407:1: warning: control reaches end of non-void function [-Wreturn-type] 407 | } | ^ r_interface.cpp: In function 'SEXPREC* r_compute_all_matching_tuples_discrete(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': r_interface.cpp:513:1: warning: control reaches end of non-void function [-Wreturn-type] 513 | } | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: r_interface.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/MDFS/src' ERROR: compilation failed for package ‘MDFS’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/MDFS-lib/MDFS’ Command exited with non-zero status 1 Time 0:09.06, 6.56 + 0.98