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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HIBAG
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HIBAG’ ...
** 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’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c HIBAG.cpp -o HIBAG.o
In file included from HIBAG.cpp:30:
HIBAG.cpp: In function ‘SEXPREC* HIBAG_AlleleStrand(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
HIBAG.cpp:336:40: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
336 | SET_ELEMENT(rv_ans, 1, ScalarInteger(out_n_stand_amb));
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:131:54: note: in definition of macro ‘SET_ELEMENT’
131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val)
| ^~~
HIBAG.cpp: In function ‘SEXPREC* HIBAG_AlleleStrand2(SEXP, SEXP)’:
HIBAG.cpp:348:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
348 | error("'allele1' and 'allele2' should have the same length.");
| ^~~~~
| perror
In file included from /home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41:
HIBAG.cpp: In function ‘SEXPREC* new_model_id(int, HLA_LIB::CAttrBag_Model*)’:
HIBAG.cpp:469:28: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
469 | SEXP ans = PROTECT(ScalarInteger(id));
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
HIBAG.cpp:472:27: error: ‘install’ was not declared in this scope
472 | Rf_setAttrib(ans, install("handle_ptr"), ptr);
| ^~~~~~~
HIBAG.cpp: In function ‘SEXPREC* HIBAG_New(SEXP, SEXP, SEXP)’:
HIBAG.cpp:490:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
490 | error("Invalid number of samples: %d.", n_samp);
| ^~~~~
| perror
HIBAG.cpp:493:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
493 | error("Invalid number of SNPs: %d.", n_snp);
| ^~~~~
| perror
HIBAG.cpp:496:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
496 | error("Invalid number of unique HLA alleles: %d.", n_hla);
| ^~~~~
| perror
HIBAG.cpp: In function ‘SEXPREC* HIBAG_Training(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
HIBAG.cpp:522:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
522 | error("Invalid number of samples: %d.", n_samp);
| ^~~~~
| perror
HIBAG.cpp:525:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
525 | error("Invalid number of SNPs: %d.", n_snp);
| ^~~~~
| perror
HIBAG.cpp:528:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
528 | error("Invalid number of unique HLA alleles: %d.", n_hla);
| ^~~~~
| perror
HIBAG.cpp: In function ‘SEXPREC* HIBAG_NewClassifierHaplo(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
HIBAG.cpp:823:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
823 | error("Invalid length of 'hla'.");
| ^~~~~
| perror
HIBAG.cpp:825:17: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
825 | error("Invalid length of 'haplo'.");
| ^~~~~
| perror
HIBAG.cpp: In function ‘SEXPREC* HIBAG_GetNumClassifiers(SEXP)’:
HIBAG.cpp:870:26: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
870 | rv_ans = ScalarInteger(_HIBAG_MODELS_[midx]->ClassifierList().size());
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
HIBAG.cpp: In function ‘SEXPREC* HIBAG_GetClassifierList(SEXP, SEXP)’:
HIBAG.cpp:933:49: error: ‘mkChar’ was not declared in this scope
933 | mkChar(Haplo.List[i].HaploToStr(nsnp).c_str()));
| ^~~~~~
HIBAG.cpp:952:53: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’?
952 | SET_ELEMENT(lst, 3, ScalarReal(M.OutOfBag_Accuracy()));
| ^~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:131:54: note: in definition of macro ‘SET_ELEMENT’
131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val)
| ^~~
HIBAG.cpp: In function ‘SEXPREC* HIBAG_BEDFlag(SEXP)’:
HIBAG.cpp:1079:26: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
1079 | rv_ans = ScalarInteger((unsigned char)prefix[2]);
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
HIBAG.cpp: In function ‘SEXPREC* HIBAG_SeqMerge(SEXP)’:
HIBAG.cpp:1203:25: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
1203 | error("Internal error in 'HIBAG_SeqMerge()'.");
| ^~~~~
| perror
HIBAG.cpp:1229:24: error: ‘mkString’ was not declared in this scope; did you mean ‘Rf_mkString’?
1229 | return mkString(ss.c_str());
| ^~~~~~~~
| Rf_mkString
HIBAG.cpp: In function ‘SEXPREC* HIBAG_SeqRmDot(SEXP, SEXP)’:
HIBAG.cpp:1270:48: error: ‘mkChar’ was not declared in this scope
1270 | SET_STRING_ELT(seq, i, mkChar(ss.c_str()));
| ^~~~~~
HIBAG.cpp:1273:40: error: ‘mkChar’ was not declared in this scope
1273 | SET_STRING_ELT(ref, 0, mkChar(ref_str.c_str()));
| ^~~~~~
HIBAG.cpp: In function ‘SEXPREC* HIBAG_Kernel_Version()’:
HIBAG.cpp:1367:33: error: ‘mkChar’ was not declared in this scope
1367 | SET_STRING_ELT(info, 0, mkChar(CPU_Info()));
| ^~~~~~
HIBAG.cpp:1417:29: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
1417 | SET_ELEMENT(ans, 2, ScalarInteger(ntot));
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:131:54: note: in definition of macro ‘SET_ELEMENT’
131 | #define SET_ELEMENT(x, i, val) SET_VECTOR_ELT(x, i, val)
| ^~~
make: *** [/home/biocbuild/bbs-3.20-bioc/R/etc/Makeconf:202: HIBAG.o] Error 1
ERROR: compilation failed for package ‘HIBAG’
* removing ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/HIBAG’
* restoring previous ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/HIBAG’
