##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data immunoClust
###
##############################################################################
##############################################################################


* checking for file ‘immunoClust/DESCRIPTION’ ... OK
* preparing ‘immunoClust’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘immunoClust’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** 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’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c R_meta.cpp -o R_meta.o
R_meta.cpp: In function ‘void _copyMixtureModel(SEXP, double*, double*, double*)’:
R_meta.cpp:111:48: error: ‘install’ was not declared in this scope
  111 |         int K = INTEGER(R_do_slot(res_cluster, install("K")))[0];
      |                                                ^~~~~~~
R_meta.cpp: In function ‘SEXPREC* _ME_ret(int, int, int)’:
R_meta.cpp:126:39: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
  126 |                 SEXP ret = Rf_protect(allocVector(VECSXP, 12));
      |                                       ^~~~~~~~~~~
      |                                       Rf_allocVector
R_meta.cpp:129:42: error: ‘mkChar’ was not declared in this scope
  129 |                 SET_STRING_ELT(names, 0, mkChar("L"));
      |                                          ^~~~~~
R_meta.cpp:156:9: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’?
  156 |         setAttrib(ret, R_NamesSymbol, names);
      |         ^~~~~~~~~
      |         Rf_setAttrib
R_meta.cpp: In function ‘SEXPREC* call_SON_combineClustering(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
R_meta.cpp:273:46: error: ‘install’ was not declared in this scope
  273 |         int G = INTEGER(R_do_slot(res_model, install("K")))[0];
      |                                              ^~~~~~~
R_meta.cpp: In function ‘SEXPREC* call_SON_normalize(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
R_meta.cpp:465:49: error: ‘install’ was not declared in this scope
  465 |         int P = INTEGER(Rf_getAttrib(res_model, install("P")))[0];
      |                                                 ^~~~~~~
R_meta.cpp:485:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
  485 |         SEXP ret = Rf_protect(allocVector(REALSXP, totK*P));
      |                               ^~~~~~~~~~~
      |                               Rf_allocVector
R_meta.cpp: In function ‘SEXPREC* call_mvnDist(SEXP, SEXP, SEXP, SEXP, SEXP)’:
R_meta.cpp:581:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
  581 |         SEXP ret = Rf_protect(allocVector(VECSXP, k*(k-1)/2));
      |                               ^~~~~~~~~~~
      |                               Rf_allocVector
R_meta.cpp:587:26: error: ‘install’ was not declared in this scope
  587 |         Rf_setAttrib(ret,install("Size"), Rf_duplicate(K));
      |                          ^~~~~~~
make: *** [/home/biocbuild/bbs-3.20-bioc/R/etc/Makeconf:202: R_meta.o] Error 1
ERROR: compilation failed for package ‘immunoClust’
* removing ‘/tmp/RtmpC4lRJF/Rinst2a8cea386cbeab/immunoClust’
      -----------------------------------
ERROR: package installation failed