############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rtreemix ### ############################################################################## ############################################################################## * checking for file ‘Rtreemix/DESCRIPTION’ ... OK * preparing ‘Rtreemix’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘Rtreemix’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Rtreemix.cc -o Rtreemix.o Rtreemix.cc:145:11: error: use of undeclared identifier 'length' int L = length(R_events); ^ Rtreemix.cc:155:22: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? PROTECT(R_events = coerceVector(R_events, STRSXP)); ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ Rtreemix.cc:191:15: error: use of undeclared identifier 'getAttrib'; did you mean 'Rf_getAttrib'? SEXP Rdim = getAttrib(R_mat, R_DimSymbol); ^~~~~~~~~ Rf_getAttrib /Library/Frameworks/R.framework/Resources/include/Rinternals.h:538:6: note: 'Rf_getAttrib' declared here SEXP Rf_getAttrib(SEXP, SEXP); ^ Rtreemix.cc:201:19: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? PROTECT(R_mat = coerceVector(R_mat,INTSXP)); ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ Rtreemix.cc:217:21: error: use of undeclared identifier 'getAttrib'; did you mean 'Rf_getAttrib'? C_mat[i][j] = R_INT_MATRIX(R_mat, i, j); ^ Rtreemix.cc:45:49: note: expanded from macro 'R_INT_MATRIX' #define R_INT_MATRIX(m,i,j) (INTEGER(m)[INTEGER(getAttrib(m, R_DimSymbol))[0] * j + i ]); ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:538:6: note: 'Rf_getAttrib' declared here SEXP Rf_getAttrib(SEXP, SEXP); ^ Rtreemix.cc:245:19: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'? PROTECT(R_mat = allocMatrix(INTSXP, C_mat.dim1(), C_mat.dim2())); ^~~~~~~~~~~ Rf_allocMatrix /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here SEXP Rf_allocMatrix(SEXPTYPE, int, int); ^ Rtreemix.cc:301:19: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'? PROTECT(R_mat = allocMatrix(REALSXP, C_mat.dim1(), C_mat.dim2())); ^~~~~~~~~~~ Rf_allocMatrix /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here SEXP Rf_allocMatrix(SEXPTYPE, int, int); ^ Rtreemix.cc:333:19: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(R_vec = allocVector(REALSXP, v.size())); ^~~~~~~~~~~ Rf_allocVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here SEXP Rf_allocVector(SEXPTYPE, R_xlen_t); ^ Rtreemix.cc:359:17: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(ans = allocVector(STRSXP, 1)); ^~~~~~~~~~~ Rf_allocVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here SEXP Rf_allocVector(SEXPTYPE, R_xlen_t); ^ Rtreemix.cc:365:28: error: use of undeclared identifier 'mkChar' SET_STRING_ELT(ans, 0, mkChar(v)); ^ Rtreemix.cc:475:20: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(result = allocVector(VECSXP, 4)); ^~~~~~~~~~~ Rf_allocVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here SEXP Rf_allocVector(SEXPTYPE, R_xlen_t); ^ Rtreemix.cc:479:24: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(list_names = allocVector(STRSXP, 4)); ^~~~~~~~~~~ Rf_allocVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here SEXP Rf_allocVector(SEXPTYPE, R_xlen_t); ^ Rtreemix.cc:481:33: error: use of undeclared identifier 'mkChar' SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model ^ Rtreemix.cc:483:33: error: use of undeclared identifier 'mkChar' SET_STRING_ELT(list_names, 1, mkChar("resp")); // the responsibilities ^ Rtreemix.cc:485:33: error: use of undeclared identifier 'mkChar' SET_STRING_ELT(list_names, 2, mkChar("pat.hat")); // the complete sample matrix (if there were some missing data) ^ Rtreemix.cc:487:33: error: use of undeclared identifier 'mkChar' SET_STRING_ELT(list_names, 3, mkChar("graphs.mixture")); // the list of the graphs each for every tree component ^ Rtreemix.cc:491:3: error: use of undeclared identifier 'setAttrib'; did you mean 'Rf_setAttrib'? setAttrib(result, R_NamesSymbol, list_names); ^~~~~~~~~ Rf_setAttrib /Library/Frameworks/R.framework/Resources/include/Rinternals.h:580:6: note: 'Rf_setAttrib' declared here SEXP Rf_setAttrib(SEXP, SEXP, SEXP); ^ Rtreemix.cc:509:31: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'? SET_VECTOR_ELT(result, 2, allocMatrix(REALSXP, 0, 0)); ^~~~~~~~~~~ Rf_allocMatrix /Library/Frameworks/R.framework/Resources/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here SEXP Rf_allocMatrix(SEXPTYPE, int, int); ^ Rtreemix.cc:515:25: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(list_graphs = allocVector(VECSXP, K)); ^~~~~~~~~~~ Rf_allocVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT' #define PROTECT(s) Rf_protect(s) ^ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here SEXP Rf_allocVector(SEXPTYPE, R_xlen_t); ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make: *** [Rtreemix.o] Error 1 ERROR: compilation failed for package ‘Rtreemix’ * removing ‘/private/tmp/RtmpJjXB7N/Rinst13380249a92f8/Rtreemix’ ----------------------------------- ERROR: package installation failed