* installing *source* package ‘miraculix’ ... ** package ‘miraculix’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether clang++ -std=gnu++14 accepts -g... yes checking which SIMD flags are available... none configure: creating ./config.status config.status: creating src/Makevars ** libs clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c 2bit.cc -o 2bit.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c 3bit.cc -o 3bit.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c AutoMiraculix.cc -o AutoMiraculix.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c Bit23.cc -o Bit23.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c Haplo.cc -o Haplo.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c MX.cc -o MX.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c MoBPS.cc -o MoBPS.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c Scalar.cc -o Scalar.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c Vector.matrix.cc -o Vector.matrix.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c hamming.cc -o hamming.o In file included from hamming.cc:178: ./error.h:35:20: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:35:36: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:35:56: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:35:73: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:36:8: error: unknown type name 'errorloc_type' extern errorloc_type ERROR_LOC; ^ ./error.h:37:8: error: unknown type name 'errorstring_type' extern errorstring_type ERRORSTRING; ^ In file included from hamming.cc:179: ./MX.h:45:8: error: unknown type name 'SEXP' extern SEXP Information, Method, Coding; // READONLY !!!! ^ ./MX.h:51:15: error: unknown type name 'SEXP' Uint *GetInfo(SEXP M); ^ ./MX.h:126:11: error: unknown type name 'SEXP' Uint Inti(SEXP X, Uint i); ^ ./MX.h:134:24: error: unknown type name 'SEXP' Uint *GetInfoUnchecked(SEXP Code); ^ hamming.cc:180:28: error: use of undeclared identifier 'ERR' void static SSEmissing() { ERR("'Hamming' needs the availablity of 'SSE2'");} ^ hamming.cc:194:1: error: unknown type name 'SEXP' SEXP zeroNthGenoH(SEXP V SNPxIndiv, SEXP V Snps, snpcoding V method) Sm ^ hamming.cc:194:19: error: unknown type name 'SEXP' SEXP zeroNthGenoH(SEXP V SNPxIndiv, SEXP V Snps, snpcoding V method) Sm ^ hamming.cc:194:37: error: unknown type name 'SEXP' SEXP zeroNthGenoH(SEXP V SNPxIndiv, SEXP V Snps, snpcoding V method) Sm ^ hamming.cc:194:70: error: use of undeclared identifier 'R_NilValue' SEXP zeroNthGenoH(SEXP V SNPxIndiv, SEXP V Snps, snpcoding V method) Sm ^ hamming.cc:181:35: note: expanded from macro 'Sm' #define Sm { SSEmissing(); return R_NilValue; } ^ hamming.cc:195:14: error: unknown type name 'SEXP' Uint *AlignH(SEXP Code, Uint nr, bool test) Su ^ 16 errors generated. make[1]: *** [hamming.o] Error 1 clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c hamming2.cc -o hamming2.o In file included from hamming2.cc:159: ./error.h:35:20: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:35:36: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:35:56: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:35:73: error: use of undeclared identifier 'LENERRMSG' extern char ERRMSG[LENERRMSG], MSG[LENERRMSG], BUG_MSG[LENERRMSG], MSG2[LENERRMSG]; ^ ./error.h:36:8: error: unknown type name 'errorloc_type' extern errorloc_type ERROR_LOC; ^ ./error.h:37:8: error: unknown type name 'errorstring_type' extern errorstring_type ERRORSTRING; ^ In file included from hamming2.cc:160: ./MX.h:45:8: error: unknown type name 'SEXP' extern SEXP Information, Method, Coding; // READONLY !!!! ^ ./MX.h:51:15: error: unknown type name 'SEXP' Uint *GetInfo(SEXP M); ^ ./MX.h:126:11: error: unknown type name 'SEXP' Uint Inti(SEXP X, Uint i); ^ ./MX.h:134:24: error: unknown type name 'SEXP' Uint *GetInfoUnchecked(SEXP Code); ^ hamming2.cc:162:3: error: use of undeclared identifier 'ERR' ERR("'Hamming' needs at least the availablity of 'SSE2'"); ^ hamming2.cc:173:1: error: unknown type name 'SEXP' SEXP matrix_startH2( Uint V snps, Uint V individuals,SEXP V file)Sm ^ hamming2.cc:173:54: error: unknown type name 'SEXP' SEXP matrix_startH2( Uint V snps, Uint V individuals,SEXP V file)Sm ^ hamming2.cc:173:66: error: use of undeclared identifier 'R_NilValue' SEXP matrix_startH2( Uint V snps, Uint V individuals,SEXP V file)Sm ^ hamming2.cc:164:35: note: expanded from macro 'Sm' #define Sm { SSEmissing(); return R_NilValue; } ^ hamming2.cc:175:55: error: unknown type name 'SEXP' Uint V start_snp, Uint V end_snp, Uint V Mnrow, SEXP V Ans, ^ hamming2.cc:180:3: error: use of undeclared identifier 'ERR' ERR("Hamming snp coding needs at least SSE2"); ^ hamming2.cc:182:1: error: unknown type name 'SEXP' SEXP get_matrixH2(SEXP V SNPxIndiv) Sm ^ hamming2.cc:182:19: error: unknown type name 'SEXP' SEXP get_matrixH2(SEXP V SNPxIndiv) Sm ^ hamming2.cc:182:37: error: use of undeclared identifier 'R_NilValue' SEXP get_matrixH2(SEXP V SNPxIndiv) Sm ^ hamming2.cc:164:35: note: expanded from macro 'Sm' #define Sm { SSEmissing(); return R_NilValue; } ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[1]: *** [hamming2.o] Error 1 clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c hamming3.cc -o hamming3.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c haplogeno.cc -o haplogeno.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c initNerror.cc -o initNerror.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c kleinkram.cc -o kleinkram.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c multiply.cc -o multiply.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c multiply256.cc -o multiply256.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c nocoding.cc -o nocoding.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c options.cc -o options.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c packed128.cc -o packed128.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c packed256.cc -o packed256.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c scan.cc -o scan.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c shuffle128.cc -o shuffle128.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c shuffle256.cc -o shuffle256.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c thuy.cc -o thuy.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c windower.cc -o windower.o clang++ -std=gnu++14 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -g -O2 -c xport_import.cc -o xport_import.o clang -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/RandomFieldsUtils/include' -I/opt/R/arm64/include -fPIC -falign-functions=8 -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c zzz.c -o zzz.o make[1]: Target `all' not remade because of errors. ERROR: compilation failed for package ‘miraculix’ * removing ‘/Users/ripley/R/packages/tests-devel/miraculix.Rcheck/miraculix’