* installing *source* package ‘GenSA’ ... ** package ‘GenSA’ 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/GenSA/src' 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 Caller.cpp -o Caller.o In file included from Caller.h:13, from Caller.cpp:9: Engine.h: In member function 'void Engine::setNoImprovementStop(int)': Engine.h:165:17: error: 'warning' was not declared in this scope; did you mean 'Rf_warning'? 165 | warning("Warning, trace mat has to be enabled to make no improvement stop criteria working"); | ^~~~~~~ | Rf_warning Engine.h: In member function 'void Engine::setUseTraceMat(bool)': Engine.h:294:17: error: 'warning' was not declared in this scope; did you mean 'Rf_warning'? 294 | warning("Trace mat has to be activated to have no improvment stop criteria to work."); | ^~~~~~~ | Rf_warning Caller.cpp: In member function 'SEXPREC* Caller::getEnergy()': Caller.cpp:15:30: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 15 | Rf_protect(returnValue = allocVector(REALSXP, 1)); | ^~~~~~~~~~~ | Rf_allocVector Caller.cpp: In member function 'SEXPREC* Caller::getXMiniVector()': Caller.cpp:26:30: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 26 | Rf_protect(returnValue = allocVector(REALSXP, engine_.getX().size())); | ^~~~~~~~~~~ | Rf_allocVector Caller.cpp:31:5: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 31 | setAttrib(returnValue, R_NamesSymbol, engine_.rEnv_->xNames); | ^~~~~~~~~ | Rf_setAttrib Caller.cpp: In member function 'SEXPREC* Caller::getTraceMat(const char*)': Caller.cpp:67:30: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 67 | Rf_protect(returnValue = allocVector(REALSXP, size)); | ^~~~~~~~~~~ | Rf_allocVector Caller.cpp: In static member function 'static SEXPREC* Caller::getListElement(SEXP, char*)': Caller.cpp:87:37: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 87 | SEXP elmt = R_NilValue, names = getAttrib(list, R_NamesSymbol); | ^~~~~~~~~ | Rf_getAttrib Caller.cpp:90:21: error: 'length' was not declared in this scope 90 | for (i = 0; i < length(list); ++i) | ^~~~~~ Caller.cpp: In member function 'void Caller::execute(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': Caller.cpp:106:13: error: 'asInteger' was not declared in this scope; did you mean 'Rf_asInteger'? 106 | asInteger(getListElement(controls_R, (char*) "markov.length"))); | ^~~~~~~~~ | Rf_asInteger Caller.cpp:112:10: error: 'isNull' was not declared in this scope 112 | if (!isNull(getListElement(controls_R, (char*) "seed"))) | ^~~~~~ Caller.cpp:129:10: error: 'isNull' was not declared in this scope 129 | if (!isNull(getListElement(controls_R, (char*) "threshold.stop"))) | ^~~~~~ Caller.cpp:134:17: error: 'asReal' was not declared in this scope 134 | asReal(getListElement(controls_R, (char*) "threshold.stop"))); | ^~~~~~ Caller.cpp:142:10: error: 'isNull' was not declared in this scope 142 | if (!isNull(getListElement(controls_R, (char*) "tem.restart"))) | ^~~~~~ Caller.cpp:146:17: error: 'asReal' was not declared in this scope 146 | asReal(getListElement(controls_R, (char*) "tem.restart"))); | ^~~~~~ Caller.cpp:154:10: error: 'isNull' was not declared in this scope 154 | if (!isNull(getListElement(controls_R, (char*) "max.time"))) | ^~~~~~ Caller.cpp:157:17: error: 'asReal' was not declared in this scope 157 | asReal(getListElement(controls_R, (char*) "max.time"))); | ^~~~~~ Caller.cpp:166:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 166 | if (asLogical(getListElement(controls_R, (char*) "smooth"))) | ^~~~~~~~~ | Rf_asLogical Caller.cpp:175:9: error: 'asLogical' was not declared in this scope; did you mean 'Rf_asLogical'? 175 | if (asLogical(getListElement(controls_R, (char*) "trace.mat"))) | ^~~~~~~~~ | Rf_asLogical Caller.cpp:193:10: error: 'isNull' was not declared in this scope 193 | if (!isNull(jc_R)) | ^~~~~~ Caller.cpp:203:10: error: 'isNull' was not declared in this scope 203 | if (!isNull(getListElement(controls_R, (char*) "simple.function"))) | ^~~~~~ Caller.cpp:228:28: error: 'asReal' was not declared in this scope 228 | engine_.setInitialTemp(asReal(getListElement(controls_R, (char*) "temperature"))); | ^~~~~~ Caller.cpp:259:18: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 259 | OS->xNames = getAttrib(x_R, R_NamesSymbol); | ^~~~~~~~~ | Rf_getAttrib In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from Utils.h:16, from Tracer.h:13, from Engine.h:15: Caller.cpp:264:24: error: 'lang2' was not declared in this scope 264 | PROTECT(OS->R_fn = lang2(fn_R, R_NilValue)); | ^~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ Caller.cpp:266:10: error: 'isNull' was not declared in this scope 266 | if (!isNull(jc_R)) | ^~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: Caller.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/GenSA/src' ERROR: compilation failed for package ‘GenSA’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/GenSA-lib/GenSA’ Command exited with non-zero status 1 Time 0:02.60, 2.09 + 0.29