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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gdsfmt
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘gdsfmt’ ...
** using staged installation
** libs
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 -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c R_CoreArray.cpp -o R_CoreArray.o
R_CoreArray.cpp: In function ‘SEXPREC* GetListElement(SEXP, const char*)’:
R_CoreArray.cpp:157:22: error: ‘getAttrib’ was not declared in this scope; did you mean ‘Rf_getAttrib’?
157 | SEXP names = getAttrib(list, R_NamesSymbol);
| ^~~~~~~~~
| Rf_getAttrib
R_CoreArray.cpp: In function ‘int GetIndexList(SEXP, const char*)’:
R_CoreArray.cpp:173:22: error: ‘getAttrib’ was not declared in this scope; did you mean ‘Rf_getAttrib’?
173 | SEXP names = getAttrib(list, R_NamesSymbol);
| ^~~~~~~~~
| Rf_getAttrib
R_CoreArray.cpp: In function ‘bool gds_verbose()’:
R_CoreArray.cpp:185:38: error: ‘install’ was not declared in this scope
185 | int v = asLogical(GetOption1(install("gds.verbose")));
| ^~~~~~~
R_CoreArray.cpp:185:27: error: ‘GetOption1’ was not declared in this scope; did you mean ‘Rf_GetOption1’?
185 | int v = asLogical(GetOption1(install("gds.verbose")));
| ^~~~~~~~~~
| Rf_GetOption1
R_CoreArray.cpp:185:17: error: ‘asLogical’ was not declared in this scope; did you mean ‘Rf_asLogical’?
185 | int v = asLogical(GetOption1(install("gds.verbose")));
| ^~~~~~~~~
| Rf_asLogical
R_CoreArray.cpp: In function ‘void gdsfile_free(SEXP)’:
R_CoreArray.cpp:216:32: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
216 | if (has_error) error("%s", GDS_GetError());
| ^~~~~
| perror
In file included from ../inst/include/R_GDS.h:44,
from ../inst/include/R_GDS_CPP.h:44,
from R_CoreArray.cpp:41:
R_CoreArray.cpp: In function ‘SEXPREC* GDS_R_Obj2SEXP(CoreArray::PdGDSObj)’:
R_CoreArray.cpp:368:31: error: ‘mkString’ was not declared in this scope; did you mean ‘Rf_mkString’?
368 | SET_CLASS(rv, mkString("gdsn.class"));
| ^~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:142:64: note: in definition of macro ‘SET_CLASS’
142 | #define SET_CLASS(x, n) Rf_setAttrib(x, R_ClassSymbol, n)
| ^
R_CoreArray.cpp: In function ‘int GDS_R_Set_Factor(CoreArray::PdGDSObj, SEXP)’:
R_CoreArray.cpp:444:51: error: ‘mkCharLenCE’ was not declared in this scope; did you mean ‘Rf_mkCharLenCE’?
444 | SET_STRING_ELT(levels, i, mkCharLenCE(&s[0], s.size(), CE_UTF8));
| ^~~~~~~~~~~
| Rf_mkCharLenCE
R_CoreArray.cpp:447:32: error: ‘mkString’ was not declared in this scope; did you mean ‘Rf_mkString’?
447 | SET_CLASS(Val, mkString("factor"));
| ^~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:142:64: note: in definition of macro ‘SET_CLASS’
142 | #define SET_CLASS(x, n) Rf_setAttrib(x, R_ClassSymbol, n)
| ^
R_CoreArray.cpp:453:43: error: ‘mkCharLenCE’ was not declared in this scope; did you mean ‘Rf_mkCharLenCE’?
453 | SET_STRING_ELT(levels, 0, mkCharLenCE(&s[0], s.size(), CE_UTF8));
| ^~~~~~~~~~~
| Rf_mkCharLenCE
R_CoreArray.cpp:455:32: error: ‘mkString’ was not declared in this scope; did you mean ‘Rf_mkString’?
455 | SET_CLASS(Val, mkString("factor"));
| ^~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:142:64: note: in definition of macro ‘SET_CLASS’
142 | #define SET_CLASS(x, n) Rf_setAttrib(x, R_ClassSymbol, n)
| ^
R_CoreArray.cpp: In function ‘SEXPREC* GDS_R_Array_Read(CoreArray::PdAbstractArray, const C_Int32*, const C_Int32*, const C_BOOL* const*, C_UInt32)’:
R_CoreArray.cpp:625:49: error: ‘mkCharLenCE’ was not declared in this scope; did you mean ‘Rf_mkCharLenCE’?
625 | mkCharLenCE(&s[0], s.size(), CE_UTF8));
| ^~~~~~~~~~~
| Rf_mkCharLenCE
R_CoreArray.cpp: In function ‘void GDS_R_Apply(int, CoreArray::CdAbstractArray**, int*, const C_BOOL* const* const*, void (*)(SEXP, C_Int32, CoreArray::CdArrayRead**, void*), void (*)(SEXP, C_Int32, void*), void*, C_BOOL, C_UInt32)’:
R_CoreArray.cpp:886:57: error: ‘mkCharLenCE’ was not declared in this scope; did you mean ‘Rf_mkCharLenCE’?
886 | mkCharLenCE(&s[0], s.size(), CE_UTF8));
| ^~~~~~~~~~~
| Rf_mkCharLenCE
R_CoreArray.cpp: In function ‘void GDS_R_Append(CoreArray::PdAbstractArray, SEXP)’:
R_CoreArray.cpp:941:51: error: ‘translateCharUTF8’ was not declared in this scope; did you mean ‘Rf_translateCharUTF8’?
941 | buf[i] = UTF8Text(translateCharUTF8(s));
| ^~~~~~~~~~~~~~~~~
| Rf_translateCharUTF8
R_CoreArray.cpp: In function ‘void GDS_R_AppendEx(CoreArray::PdAbstractArray, SEXP, size_t, size_t)’:
R_CoreArray.cpp:987:51: error: ‘translateCharUTF8’ was not declared in this scope; did you mean ‘Rf_translateCharUTF8’?
987 | buf[i] = UTF8Text(translateCharUTF8(s));
| ^~~~~~~~~~~~~~~~~
| Rf_translateCharUTF8
R_CoreArray.cpp: In function ‘void GDS_R_Is_Element(CoreArray::PdAbstractArray, SEXP, C_BOOL*)’:
R_CoreArray.cpp:1036:42: error: ‘translateCharUTF8’ was not declared in this scope; did you mean ‘Rf_translateCharUTF8’?
1036 | SetString.insert(translateCharUTF8(STRING_ELT(SetEL, i)));
| ^~~~~~~~~~~~~~~~~
| Rf_translateCharUTF8
R_CoreArray.cpp: In function ‘C_BOOL GDS_File_Reopen(SEXP)’:
R_CoreArray.cpp:1263:27: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
1263 | SEXP ID = ScalarInteger(GetFileIndex(file));
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
R_CoreArray.cpp: In function ‘void check_load_pkg_matrix()’:
R_CoreArray.cpp:1810:25: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
1810 | error("Fail to load the Matrix package!");
| ^~~~~
| perror
In file included from /home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41:
R_CoreArray.cpp: In function ‘SEXPREC* GDS_New_SpCMatrix(const double*, const int*, const int*, int, int, int)’:
R_CoreArray.cpp:1853:27: error: ‘eval’ was not declared in this scope
1853 | SEXP rv = PROTECT(eval(epr, R_GlobalEnv));
| ^~~~
/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)
| ^
R_CoreArray.cpp: In function ‘SEXPREC* GDS_New_SpCMatrix2(SEXP, SEXP, SEXP, int, int)’:
R_CoreArray.cpp:1870:27: error: ‘eval’ was not declared in this scope
1870 | SEXP rv = PROTECT(eval(epr, R_GlobalEnv));
| ^~~~
/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)
| ^
make: *** [/home/biocbuild/bbs-3.20-bioc/R/etc/Makeconf:202: R_CoreArray.o] Error 1
ERROR: compilation failed for package ‘gdsfmt’
* removing ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt’
* restoring previous ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/gdsfmt’
