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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ternarynet
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'ternarynet' ...
** this is package 'ternarynet' version '1.51.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c array.c -o array.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c gn_Rwrap.c -o gn_Rwrap.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/include/R.h:69,
                 from gn_Rwrap.h:4,
                 from gn_Rwrap.c:1:
E:/biocbuild/bbs-3.21-bioc/R/include/R_ext/Arith.h:58:25: warning: 'R_NaReal' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
   58 | #define NA_REAL         R_NaReal
      |                         ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rmath.h:796:17: note: in expansion of macro 'NA_REAL'
  796 | R_EXTERN double NA_REAL;
      |                 ^~~~~~~
In file included from gn_Rwrap.c:9:
E:/biocbuild/bbs-3.21-bioc/R/include/Rmath.h:797:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
  797 | R_EXTERN double R_PosInf;
      |                 ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rmath.h:798:17: warning: 'R_NegInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
  798 | R_EXTERN double R_NegInf;
      |                 ^~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c init.c -o init.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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 E:/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));
      |                       ^~~~~~~~~~~
E:/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; did you mean 'char'?
  320 |     SET_STRING_ELT(Rnames,0,mkChar("degreeObj"));
      |                             ^~~~~~
      |                             char
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: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:294: tnetfit.o] Error 1
ERROR: compilation failed for package 'ternarynet'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/ternarynet'