* installing *source* package ‘topicmodels’ ... ** package ‘topicmodels’ 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/topicmodels/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 cokus.c -o cokus.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 common.c -o common.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 ctm.c -o ctm.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 dataset.cpp -o dataset.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 gsl-wrappers.c -o gsl-wrappers.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 inference.c -o inference.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 init.c -o init.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 lda-alpha.c -o lda-alpha.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 lda-inference.c -o lda-inference.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 lda-model.c -o lda-model.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 model.cpp -o model.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 rGibbslda.cpp -o rGibbslda.o In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from rGibbslda.cpp:55: rGibbslda.cpp: In function 'SEXPREC* returnObjectGibbsLDA(SEXP, model*)': rGibbslda.cpp:65:16: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 65 | tp = PROTECT(allocVector(INTSXP, 1)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ rGibbslda.cpp:67:17: error: 'install' was not declared in this scope 67 | SET_SLOT(ans, install("iter"), tp); | ^~~~~~~ /data/gannet/ripley/R/R-devel/include/Rdefines.h:152:55: note: in definition of macro 'SET_SLOT' 152 | #define SET_SLOT(x, what, value) R_do_slot_assign(x, what, value) | ^~~~ rGibbslda.cpp:86:16: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 86 | tp = PROTECT(allocMatrix(REALSXP, model->K, model->V)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ rGibbslda.cpp:163:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'? 163 | setAttrib(wordassign, R_NamesSymbol, nms = allocVector(STRSXP, 5)); | ^~~~~~~~~ | Rf_setAttrib rGibbslda.cpp:164:26: error: 'mkChar' was not declared in this scope 164 | SET_STRING_ELT(nms, 0, mkChar("i")); | ^~~~~~ rGibbslda.cpp:169:40: error: 'mkString' was not declared in this scope; did you mean 'Rf_mkString'? 169 | setAttrib(wordassign, R_ClassSymbol, mkString("simple_triplet_matrix")); | ^~~~~~~~ | Rf_mkString rGibbslda.cpp: In function 'SEXPREC* rGibbslda(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': rGibbslda.cpp:198:63: error: 'install' was not declared in this scope 198 | if (*INTEGER(initialize) == 1 || *INTEGER(GET_SLOT(control, install("estimate.beta"))) == 0) { | ^~~~~~~ /data/gannet/ripley/R/R-devel/include/Rdefines.h:151:46: note: in definition of macro 'GET_SLOT' 151 | #define GET_SLOT(x, what) R_do_slot(x, what) | ^~~~ rGibbslda.cpp:207:36: error: 'install' was not declared in this scope 207 | delta = REAL(GET_SLOT(control, install("delta"))); | ^~~~~~~ /data/gannet/ripley/R/R-devel/include/Rdefines.h:151:46: note: in definition of macro 'GET_SLOT' 151 | #define GET_SLOT(x, what) R_do_slot(x, what) | ^~~~ rGibbslda.cpp:215:48: error: 'install' was not declared in this scope 215 | *INTEGER(GET_SLOT(control, install("iter"))), | ^~~~~~~ /data/gannet/ripley/R/R-devel/include/Rdefines.h:151:46: note: in definition of macro 'GET_SLOT' 151 | #define GET_SLOT(x, what) R_do_slot(x, what) | ^~~~ rGibbslda.cpp:227:26: error: 'asChar' was not declared in this scope 227 | CHAR(asChar(prefix)), | ^~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:200:24: note: in definition of macro 'CHAR' 200 | #define CHAR(x) R_CHAR(x) | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: rGibbslda.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/topicmodels/src' ERROR: compilation failed for package ‘topicmodels’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/topicmodels-lib/topicmodels’ Command exited with non-zero status 1 Time 0:09.05, 7.81 + 0.99