############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/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: ‘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 array.c -o array.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c gn.c -o gn.o gn.c: In function ‘score’: gn.c:486: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 486 | #pragma omp parallel for | gn.c:493: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas] 493 | #pragma omp atomic | gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c gn_Rwrap.c -o gn_Rwrap.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c init.c -o init.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 tnetfit.cc -o tnetfit.o tnetfit.cc: In function ‘SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: tnetfit.cc:35:32: error: ‘coerceVector’ was not declared in this scope; did you mean ‘Rf_coerceVector’? 35 | perturbationType = INTEGER(coerceVector(RperturbationType, INTSXP))[0]; | ^~~~~~~~~~~~ | Rf_coerceVector In file included from /home/biocbuild/bbs-3.21-bioc/R/include/Rdefines.h:41, from tnetfit.cc:12: tnetfit.cc:220:23: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’? 220 | PROTECT(Routput = allocVector(VECSXP, 14)); | ^~~~~~~~~~~ /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) | ^ tnetfit.cc:311:33: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’? 311 | SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore)); | ^~~~~~~~~~ | Rf_ScalarReal tnetfit.cc:315:33: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’? 315 | SET_VECTOR_ELT(Routput, 12, ScalarInteger(stage_count)); | ^~~~~~~~~~~~~ | Rf_ScalarInteger tnetfit.cc:320:29: error: ‘mkChar’ was not declared in this scope 320 | SET_STRING_ELT(Rnames,0,mkChar("degreeObj")); | ^~~~~~ tnetfit.cc:334:5: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’? 334 | setAttrib(Routput, R_NamesSymbol, Rnames); | ^~~~~~~~~ | Rf_setAttrib tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable] 73 | int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; | ^~~~~ make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:200: tnetfit.o] Error 1 ERROR: compilation failed for package ‘ternarynet’ * removing ‘/tmp/RtmpOp4V2T/Rinst13d0d522a66b87/ternarynet’ ----------------------------------- ERROR: package installation failed