* installing *source* package ‘rjags’ ... ** package ‘rjags’ successfully unpacked and MD5 sums checked ** using staged installation checking for pkg-config... /usr/bin/pkg-config configure: Setting compile and link flags according to pkg-config configure: Compile flags are -I/usr/local/include/JAGS configure: Link flags are -L/usr/local/lib64 -ljags checking for gcc... gcc-13 checking whether we are using the GNU C compiler... no checking whether gcc-13 accepts -g... no checking for gcc-13 option to accept ISO C89... unsupported checking for jags_version in -ljags... yes checking version of JAGS library... OK configure: creating ./config.status config.status: creating src/Makevars configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/unix/zzz.R ** 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/rjags/src' gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include/JAGS -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 init.c -o init.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include/JAGS -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 jags.cc -o jags.o jags.cc: In function 'void checkConsole(SEXP)': jags.cc:74:36: error: 'install' was not declared in this scope 74 | static SEXP JAGS_console_tag = install("JAGS_CONSOLE_TAG"); | ^~~~~~~ jags.cc:78:9: error: 'error' was not declared in this scope; did you mean 'perror'? 78 | error("bad JAGS console pointer"); | ^~~~~ | perror jags.cc: In function 'int intArg(SEXP)': jags.cc:84:10: error: 'isNumeric' was not declared in this scope; did you mean 'Rf_isNumeric'? 84 | if (!isNumeric(arg)) { | ^~~~~~~~~ | Rf_isNumeric jags.cc:85:9: error: 'error' was not declared in this scope; did you mean 'perror'? 85 | error("Invalid integer parameter"); | ^~~~~ | perror jags.cc: In function 'const char* stringArg(SEXP, unsigned int)': jags.cc:97:10: error: 'isString' was not declared in this scope; did you mean 'string'? 97 | if (!isString(arg)) { | ^~~~~~~~ | string jags.cc:98:9: error: 'error' was not declared in this scope; did you mean 'perror'? 98 | error("Invalid string parameter"); | ^~~~~ | perror jags.cc: In function 'bool boolArg(SEXP)': jags.cc:105:10: error: 'isLogical' was not declared in this scope; did you mean 'Rf_isLogical'? 105 | if (!isLogical(arg)) { | ^~~~~~~~~ | Rf_isLogical jags.cc:106:9: error: 'error' was not declared in this scope; did you mean 'perror'? 106 | error("Invalid logical parameter"); | ^~~~~ | perror jags.cc: In function 'jags::Console* ptrArg(SEXP)': jags.cc:116:9: error: 'error' was not declared in this scope; did you mean 'perror'? 116 | error("JAGS model must be recompiled"); | ^~~~~ | perror jags.cc: In function 'void printMessages(bool)': jags.cc:134:13: error: 'warning' was not declared in this scope 134 | warning("%s\n", msg.c_str()); | ^~~~~~~ jags.cc:140:13: error: 'error' was not declared in this scope; did you mean 'perror'? 140 | error("%s\n", msg.c_str()); | ^~~~~ | perror jags.cc:143:13: error: 'error' was not declared in this scope; did you mean 'perror'? 143 | error("Internal error in JAGS library"); | ^~~~~ | perror jags.cc: In function 'void setSArrayValue(jags::SArray&, SEXP)': jags.cc:150:22: error: 'length' was not declared in this scope 150 | vector v(length(e)); | ^~~~~~ jags.cc: In function 'void writeDataTable(SEXP, std::map, jags::SArray>&)': jags.cc:164:18: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 164 | SEXP names = getAttrib(data, R_NamesSymbol); | ^~~~~~~~~ | Rf_getAttrib jags.cc:165:10: error: 'isNewList' was not declared in this scope; did you mean 'Rf_isNewList'? 165 | if (!isNewList(data)) { | ^~~~~~~~~ | Rf_isNewList jags.cc:166:9: error: 'error' was not declared in this scope; did you mean 'perror'? 166 | error("data must be a list"); | ^~~~~ | perror jags.cc:168:9: error: 'length' was not declared in this scope 168 | if (length(names) != length(data)) { | ^~~~~~ jags.cc:169:9: error: 'error' was not declared in this scope; did you mean 'perror'? 169 | error("data must be a named list"); | ^~~~~ | perror jags.cc:172:25: error: 'length' was not declared in this scope 172 | for (int i = 0; i < length(data); ++i) { | ^~~~~~ jags.cc: In function 'jags::SimpleRange makeRange(SEXP, SEXP)': jags.cc:203:9: error: 'length' was not declared in this scope 203 | if (length(lower) != length(upper)) { | ^~~~~~ jags.cc:204:9: error: 'error' was not declared in this scope; did you mean 'perror'? 204 | error("length mismatch between lower and upper limits"); | ^~~~~ | perror jags.cc:206:13: error: 'length' was not declared in this scope 206 | int n = length(lower); | ^~~~~~ jags.cc:221:9: error: 'error' was not declared in this scope; did you mean 'perror'? 221 | error("Invalid range"); | ^~~~~ | perror In file included from jags.cc:62: jags.cc: In function 'SEXPREC* readDataTable(const std::map, jags::SArray>&)': jags.cc:232:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 232 | PROTECT(data = allocVector(VECSXP, 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) | ^ jags.cc:272:49: error: 'mkChar' was not declared in this scope 272 | SET_STRING_ELT(dimnames, k, mkChar(names[k].c_str())); | ^~~~~~ jags.cc:274:17: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 274 | setAttrib(dim, R_NamesSymbol, dimnames); | ^~~~~~~~~ | Rf_setAttrib jags.cc:301:44: error: 'mkChar' was not declared in this scope 301 | mkChar(names_k[l].c_str())); | ^~~~~~ jags.cc:306:17: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 306 | setAttrib(e, R_DimNamesSymbol, sdimnames); | ^~~~~~~~~ | Rf_setAttrib jags.cc:317:44: error: 'mkChar' was not declared in this scope 317 | SET_STRING_ELT(snames, l, mkChar(names[l].c_str())); | ^~~~~~ jags.cc:319:13: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 319 | setAttrib(e, R_NamesSymbol, snames); | ^~~~~~~~~ | Rf_setAttrib jags.cc:331:34: error: 'mkChar' was not declared in this scope 331 | SET_STRING_ELT(names, i, mkChar(p->first.c_str())); | ^~~~~~ jags.cc:333:5: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 333 | setAttrib(data, R_NamesSymbol, names); | ^~~~~~~~~ | Rf_setAttrib jags.cc: In function 'jags::FactoryType asFactoryType(SEXP)': jags.cc:352:9: error: 'error' was not declared in this scope; did you mean 'perror'? 352 | error("Invalid factory type"); | ^~~~~ | perror jags.cc: In function 'SEXPREC* make_console()': jags.cc:394:41: error: 'install' was not declared in this scope 394 | SEXP ptr = R_MakeExternalPtr(p, install("JAGS_CONSOLE_TAG"), | ^~~~~~~ jags.cc: In function 'SEXPREC* compileR(SEXP, SEXP, SEXP, SEXP)': jags.cc:421:14: error: 'isNumeric' was not declared in this scope; did you mean 'Rf_isNumeric'? 421 | if (!isNumeric(nchain)) { | ^~~~~~~~~ | Rf_isNumeric jags.cc:422:13: error: 'error' was not declared in this scope; did you mean 'perror'? 422 | error("nchain must be numeric"); | ^~~~~ | perror jags.cc:424:14: error: 'isVector' was not declared in this scope; did you mean 'vector'? 424 | if (!isVector(data)) { | ^~~~~~~~ | vector jags.cc:425:13: error: 'error' was not declared in this scope; did you mean 'perror'? 425 | error("invalid data"); | ^~~~~ | perror jags.cc: In function 'SEXPREC* check_adaptation(SEXP)': jags.cc:464:16: error: 'ScalarLogical' was not declared in this scope; did you mean 'Rf_ScalarLogical'? 464 | return ScalarLogical(status); | ^~~~~~~~~~~~~ | Rf_ScalarLogical jags.cc: In function 'SEXPREC* is_adapting(SEXP)': jags.cc:470:16: error: 'ScalarLogical' was not declared in this scope; did you mean 'Rf_ScalarLogical'? 470 | return ScalarLogical(console->isAdapting()); | ^~~~~~~~~~~~~ | Rf_ScalarLogical jags.cc: In function 'SEXPREC* set_monitors(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': jags.cc:494:14: error: 'isString' was not declared in this scope; did you mean 'string'? 494 | if (!isString(names)) { | ^~~~~~~~ | string jags.cc:495:13: error: 'error' was not declared in this scope; did you mean 'perror'? 495 | error("names must be a character vector"); | ^~~~~ | perror jags.cc:498:17: error: 'length' was not declared in this scope 498 | int n = length(names); | ^~~~~~ jags.cc:500:13: error: 'error' was not declared in this scope; did you mean 'perror'? 500 | error("length of names must match length of lower and upper"); | ^~~~~ | perror jags.cc:504:26: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 504 | PROTECT(status = allocVector(LGLSXP, 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) | ^ jags.cc: In function 'SEXPREC* get_state(SEXP)': jags.cc:565:23: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 565 | PROTECT(ans = allocVector(VECSXP, nchain)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ jags.cc:573:26: error: 'length' was not declared in this scope 573 | int nparam = length(params); | ^~~~~~ jags.cc:574:26: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'? 574 | SEXP names = getAttrib(params, R_NamesSymbol); | ^~~~~~~~~ | Rf_getAttrib jags.cc:585:31: error: 'mkString' was not declared in this scope; did you mean 'string'? 585 | PROTECT(rngname = mkString(srng.c_str())); | ^~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ jags.cc:587:44: error: 'mkChar' was not declared in this scope 587 | SET_STRING_ELT(namesn, nparam, mkChar(".RNG.name")); | ^~~~~~ jags.cc:588:13: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 588 | setAttrib(staten, R_NamesSymbol, namesn); | ^~~~~~~~~ | Rf_setAttrib jags.cc: In function 'SEXPREC* get_variable_names(SEXP)': jags.cc:603:28: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 603 | PROTECT(varnames = allocVector(STRSXP,namevec.size())); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ jags.cc:605:41: error: 'mkChar' was not declared in this scope 605 | SET_STRING_ELT(varnames, i, mkChar(namevec[i].c_str())); | ^~~~~~ jags.cc: In function 'SEXPREC* get_samplers(SEXP)': jags.cc:620:29: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 620 | PROTECT(node_list = allocVector(VECSXP, 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) | ^ jags.cc:628:38: error: 'mkChar' was not declared in this scope 628 | SET_STRING_ELT(e, j, mkChar(samplers[i][j+1].c_str())); | ^~~~~~ jags.cc:631:46: error: 'mkChar' was not declared in this scope 631 | SET_STRING_ELT(sampler_names, i, mkChar(samplers[i][0].c_str())); | ^~~~~~ jags.cc:634:9: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 634 | setAttrib(node_list, R_NamesSymbol, sampler_names); | ^~~~~~~~~ | Rf_setAttrib jags.cc: In function 'SEXPREC* get_factories(SEXP)': jags.cc:646:28: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 646 | PROTECT(fac_list = allocVector(VECSXP, 2)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ jags.cc:652:38: error: 'mkChar' was not declared in this scope 652 | SET_STRING_ELT(names, i, mkChar(factories[i].first.c_str())); | ^~~~~~ jags.cc:662:38: error: 'mkChar' was not declared in this scope 662 | SET_STRING_ELT(fac_names, 0, mkChar("factory")); | ^~~~~~ jags.cc:664:9: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 664 | setAttrib(fac_list, R_NamesSymbol, fac_names); | ^~~~~~~~~ | Rf_setAttrib jags.cc: In function 'SEXPREC* get_iter(SEXP)': jags.cc:680:16: error: 'ScalarInteger' was not declared in this scope; did you mean 'Rf_ScalarInteger'? 680 | return ScalarInteger(ptrArg(ptr)->iter()); | ^~~~~~~~~~~~~ | Rf_ScalarInteger jags.cc: In function 'SEXPREC* get_nchain(SEXP)': jags.cc:685:16: error: 'ScalarInteger' was not declared in this scope; did you mean 'Rf_ScalarInteger'? 685 | return ScalarInteger(ptrArg(ptr)->nchain()); | ^~~~~~~~~~~~~ | Rf_ScalarInteger jags.cc: In function 'SEXPREC* load_module(SEXP)': jags.cc:690:16: error: 'ScalarLogical' was not declared in this scope; did you mean 'Rf_ScalarLogical'? 690 | return ScalarLogical(Console::loadModule(stringArg(name))); | ^~~~~~~~~~~~~ | Rf_ScalarLogical jags.cc: In function 'SEXPREC* unload_module(SEXP)': jags.cc:695:16: error: 'ScalarLogical' was not declared in this scope; did you mean 'Rf_ScalarLogical'? 695 | return ScalarLogical(Console::unloadModule(stringArg(name))); | ^~~~~~~~~~~~~ | Rf_ScalarLogical jags.cc: In function 'SEXPREC* get_modules()': jags.cc:703:28: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 703 | PROTECT(mod_list = allocVector(STRSXP, 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) | ^ jags.cc:705:41: error: 'mkChar' was not declared in this scope 705 | SET_STRING_ELT(mod_list, i, mkChar(modules[i].c_str())); | ^~~~~~ jags.cc: In function 'SEXPREC* get_version()': jags.cc:713:16: error: 'mkString' was not declared in this scope; did you mean 'string'? 713 | return mkString(jags_version()); | ^~~~~~~~ | string make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:200: jags.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/rjags/src' ERROR: compilation failed for package ‘rjags’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/rjags-lib/rjags’ Command exited with non-zero status 1 Time 0:09.97, 4.87 + 2.16