############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL cn.farms ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘cn.farms’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c R_init_cnfarms.c -o R_init_cnfarms.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c laplace.cpp -o laplace.o In file included from laplace.cpp:7: laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: laplace.cpp:448:23: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’? 448 | PROTECT(RET = allocVector(VECSXP, 8)); | ^~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ laplace.cpp:519:37: error: ‘mkChar’ was not declared in this scope 519 | SET_STRING_ELT(namesRET, 0, mkChar("normConst")); | ^~~~~~ laplace.cpp:528:9: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’? 528 | setAttrib(RET, R_NamesSymbol, namesRET); | ^~~~~~~~~ | Rf_setAttrib laplace.cpp:442:13: warning: unused variable ‘method’ [-Wunused-variable] 442 | int method=0; | ^~~~~~ laplace.cpp: In function ‘SEXPREC* momentsIntegrationTrapez(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: laplace.cpp:603:23: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’? 603 | PROTECT(RET = allocVector(VECSXP, 8)); | ^~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’ 388 | #define PROTECT(s) Rf_protect(s) | ^ laplace.cpp:708:37: error: ‘mkChar’ was not declared in this scope 708 | SET_STRING_ELT(namesRET, 0, mkChar("normConst")); | ^~~~~~ laplace.cpp:717:9: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’? 717 | setAttrib(RET, R_NamesSymbol, namesRET); | ^~~~~~~~~ | Rf_setAttrib make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: laplace.o] Error 1 ERROR: compilation failed for package ‘cn.farms’ * removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/cn.farms’ * restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/cn.farms’