############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ternarynet ### ############################################################################## ############################################################################## * checking for file ‘ternarynet/DESCRIPTION’ ... OK * preparing ‘ternarynet’: * checking DESCRIPTION meta-information ... OK * cleaning src * running ‘cleanup’ * installing the package to build vignettes ----------------------------------- * installing *source* package ‘ternarynet’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array.c -o array.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn.c -o gn.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn_Rwrap.c -o gn_Rwrap.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c tnetfit.cc -o tnetfit.o tnetfit.cc:35:32: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? perturbationType = INTEGER(coerceVector(RperturbationType, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:36:25: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? scoreType = INTEGER(coerceVector(RscoreType, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:37:27: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? backupStage = INTEGER(coerceVector(RbackupStage, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:38:24: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? maxStage = INTEGER(coerceVector(RmaxStage, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:39:29: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? maxTransition = INTEGER(coerceVector(RmaxTransition, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:41:20: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? beta = INTEGER(coerceVector(Rbeta, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:44:18: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? ne = INTEGER(coerceVector(Rne, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:45:18: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? m0 = INTEGER(coerceVector(Rm0, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:46:25: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? maxDegree = INTEGER(coerceVector(RmaxDegree, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:49:30: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? neighborDegree = INTEGER(coerceVector(RneighborDegree, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:51:21: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? nGene = INTEGER(coerceVector(RnGene, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:52:27: error: use of undeclared identifier 'coerceVector'; did you mean 'Rf_coerceVector'? nExperiment = INTEGER(coerceVector(RnExperiment, INTSXP))[0]; ^~~~~~~~~~~~ Rf_coerceVector /Library/Frameworks/R.framework/Resources/include/Rinternals.h:482:6: note: 'Rf_coerceVector' declared here SEXP Rf_coerceVector(SEXP, SEXPTYPE); ^ tnetfit.cc:220:23: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(Routput = allocVector(VECSXP, 14)); ^~~~~~~~~~~ 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); ^ tnetfit.cc:223:26: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(RdegreeObj = allocVector(INTSXP, nGene)); ^~~~~~~~~~~ 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); ^ tnetfit.cc:229:25: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(RgraphObj = allocVector(INTSXP, nGene*nGene)); ^~~~~~~~~~~ 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); ^ tnetfit.cc:242:25: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(RtableObj = allocVector(INTSXP, tableWidth*nGene)); ^~~~~~~~~~~ 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); ^ tnetfit.cc:256:29: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(RdegreeObjMin = allocVector(INTSXP, nGene)); ^~~~~~~~~~~ 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); ^ tnetfit.cc:262:28: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(RgraphObjMin = allocVector(INTSXP, nGene*nGene)); ^~~~~~~~~~~ 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); ^ tnetfit.cc:275:28: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'? PROTECT(RtableObjMin = allocVector(INTSXP, tableWidth*nGene)); ^~~~~~~~~~~ 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: *** [tnetfit.o] Error 1 ERROR: compilation failed for package ‘ternarynet’ * removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpXgnsT7/Rinst767e1a179a65/ternarynet’ ----------------------------------- ERROR: package installation failed