* installing *source* package ‘sem’ ... ** package ‘sem’ successfully unpacked and MD5 sums checked ** using staged installation ** 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/sem/src' gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c csemnlm.c -o csemnlm.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c uncmin.c -o uncmin.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -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 csem.cpp -o csem.o In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from csem.h:53, from csem.cpp:38: csem.cpp: In function 'void semprintRealVector(const double*, int, int)': csem.cpp:59:33: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 59 | PROTECT(rargs = allocVector(REALSXP,n)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ csem.cpp:65:33: error: 'lang2' was not declared in this scope 65 | PROTECT(Rcall = lang2(thefun,rargs)); | ^~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ csem.cpp:66:34: error: 'eval' was not declared in this scope 66 | PROTECT(result = eval(Rcall,theenv)); | ^~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ csem.cpp: In function 'SEXPREC* getListElement(SEXP, int)': csem.cpp:80:38: error: 'length' was not declared in this scope 80 | if(ind >= 0 && ind < length(list)) | ^~~~~~ csem.cpp:85:33: error: 'error' was not declared in this scope; did you mean 'perror'? 85 | error(("The index is not in the range of the list.")); | ^~~~~ | perror csem.cpp: In function 'SEXPREC* getListElement(SEXP, std::string)': csem.cpp:92:49: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 92 | SEXP elmt = R_NilValue, names = getAttrib(list, R_NamesSymbol); | ^~~~~~~~~ | Rf_getAttrib csem.cpp:94:33: error: 'length' was not declared in this scope 94 | for (i = 0; i < length(list); i++) | ^~~~~~ csem.cpp: In function 'double getVectorElement(SEXP, int)': csem.cpp:105:38: error: 'length' was not declared in this scope 105 | if(ind >= 0 && ind < length(vect)) | ^~~~~~ csem.cpp:108:33: error: 'error' was not declared in this scope; did you mean 'perror'? 108 | error(("The index is not in the range of the vector.")); | ^~~~~ | perror csem.cpp: In function 'double getVectorElement(SEXP, std::string)': csem.cpp:115:30: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 115 | SEXP names = getAttrib(vect, R_NamesSymbol); | ^~~~~~~~~ | Rf_getAttrib csem.cpp:118:33: error: 'length' was not declared in this scope 118 | for (i = 0; i < length(vect); i++) | ^~~~~~ csem.cpp: In function 'SEXPREC* generateMatrix(double*, int, int)': csem.cpp:129:24: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 129 | elmt = allocMatrix(REALSXP, nrow, ncol); | ^~~~~~~~~~~ | Rf_allocMatrix csem.cpp: In function 'void setApplicationOptions(int&, double&, double&, double&, int&, int&, int&, int&, double&, SEXP)': csem.cpp:214:46: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 214 | PROTECT(opts_integer_names = getAttrib(opts_integer, R_NamesSymbol)); | ^~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ csem.cpp:215:46: error: 'length' was not declared in this scope 215 | for (int list_cnt=0;list_cntfixed); | ^~~~~~ csem.cpp:607:43: error: 'nrows' was not declared in this scope 607 | double *ram5 = new double[nrows(model->ram)]; | ^~~~~ csem.cpp: In function 'void objectiveML(int, const double*, double*, double*, double*, double*, double*, double*, function_info*)': csem.cpp:868:45: error: 'nrows' was not declared in this scope 868 | MatrixMulti(REAL(model->J), nrows(model->J), ncols(model->J), invA, m, m, C0); | ^~~~~ csem.cpp:868:62: error: 'ncols' was not declared in this scope 868 | MatrixMulti(REAL(model->J), nrows(model->J), ncols(model->J), invA, m, m, C0); | ^~~~~ csem.cpp:953:38: error: 'length' was not declared in this scope 953 | nA = length(model->arrows_1_free)/2; | ^~~~~~ csem.cpp: In function 'void objectiveGLS(int, const double*, double*, double*, double*, double*, double*, double*, function_info*)': csem.cpp:1115:45: error: 'nrows' was not declared in this scope 1115 | MatrixMulti(REAL(model->J), nrows(model->J), ncols(model->J), invA, m, m, C0); | ^~~~~ csem.cpp:1115:62: error: 'ncols' was not declared in this scope 1115 | MatrixMulti(REAL(model->J), nrows(model->J), ncols(model->J), invA, m, m, C0); | ^~~~~ csem.cpp: In function 'void objectiveFIML(int, const double*, double*, double*, double*, double*, double*, double*, function_info*)': csem.cpp:1270:45: error: 'nrows' was not declared in this scope 1270 | MatrixMulti(REAL(model->J), nrows(model->J), ncols(model->J), invA, m, m, C0); | ^~~~~ csem.cpp:1270:62: error: 'ncols' was not declared in this scope 1270 | MatrixMulti(REAL(model->J), nrows(model->J), ncols(model->J), invA, m, m, C0); | ^~~~~ csem.cpp:1290:39: error: 'length' was not declared in this scope 1290 | int Npattern_number = length(model->pattern_number); // equal to nrows(model->data) | ^~~~~~ csem.cpp: In function 'void objectivelogLik(int, const double*, double*, double*, double*, double*, double*, double*, function_info*)': csem.cpp:1617:32: error: 'ncols' was not declared in this scope 1617 | int ncolData = ncols(semObject->data); | ^~~~~ csem.cpp:1629:31: error: 'nrows' was not declared in this scope; did you mean 'nrowTri'? 1629 | int nrowTri = nrows(semObject->tri); | ^~~~~ | nrowTri csem.cpp:1630:36: error: 'length' was not declared in this scope 1630 | int *tri = new int[length(semObject->tri)]; | ^~~~~~ csem.cpp: In function 'SEXPREC* csemSolve(SEXP)': csem.cpp:1928:70: error: 'length' was not declared in this scope 1928 | model->arrows_1_seq = (int *)R_alloc(length(st), sizeof(int)); | ^~~~~~ csem.cpp:1952:61: error: 'error' was not declared in this scope; did you mean 'perror'? 1952 | if(LENGTH(sx0) != model->t) error(("The number of variables are not consistent!\n")); | ^~~~~ | perror csem.cpp:2041:65: error: 'error' was not declared in this scope; did you mean 'perror'? 2041 | if(LENGTH(sx0) != semObject->t) error(("The number of variables are not consistent!\n")); | ^~~~~ | perror csem.cpp: In function 'SEXPREC* cmsemSolve(SEXP)': csem.cpp:2214:45: error: 'length' was not declared in this scope 2214 | gmodel->t = length(model->sel_free); | ^~~~~~ csem.cpp:2237:60: error: 'nrows' was not declared in this scope; did you mean 'nrow'? 2237 | int nrow = nrows(gmodel->S); | ^~~~~ | nrow csem.cpp:2238:60: error: 'ncols' was not declared in this scope; did you mean 'ncol'? 2238 | int ncol = ncols(gmodel->S); | ^~~~~ | ncol csem.cpp:2273:45: error: 'error' was not declared in this scope; did you mean 'perror'? 2273 | if(LENGTH(sx0) != model->t) error(("The number of variables are not consistent!\n")); | ^~~~~ | perror csem.cpp: At global scope: csem.cpp:787:16: warning: 'double* ExtendMatrix(const double*, const int&, const int&, const int*, const int&)' defined but not used [-Wunused-function] 787 | static double *ExtendMatrix(const double *selA, const int &row, const int &col, const int *sel, const int &nsel) | ^~~~~~~~~~~~ csem.cpp:687:13: warning: 'int* SubMatrixRow(SEXP, const int&, const int&, const int&)' defined but not used [-Wunused-function] 687 | static int *SubMatrixRow(SEXP A, const int &row, const int &col, const int &ithrow) | ^~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: csem.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/sem/src' ERROR: compilation failed for package ‘sem’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/sem-lib/sem’ Command exited with non-zero status 1 Time 0:08.18, 7.12 + 0.47