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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ternarynet
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ternarynet’ ...
** this is package ‘ternarynet’ version ‘1.51.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c array.c -o array.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c gn.c -o gn.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c gn_Rwrap.c -o gn_Rwrap.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -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
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:200: tnetfit.o] Error 1
ERROR: compilation failed for package ‘ternarynet’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/ternarynet’