############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HIBAG ### ############################################################################## ############################################################################## * checking for file ‘HIBAG/DESCRIPTION’ ... OK * preparing ‘HIBAG’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘HIBAG’ ... ** using staged installation ** libs clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HIBAG.cpp -o HIBAG.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA.cpp -o LibHLA.o LibHLA.cpp:1240:7: warning: variable 'cpu_auto_avx2' set but not used [-Wunused-but-set-variable] bool cpu_auto_avx2, cpu_max; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o LibHLA_ext_avx.cpp:529:6: error: out-of-line definition of '_PrepHaploMatch_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_PrepHaploMatch_def'? void SIMD_NAME(CAlg_Prediction::_PrepHaploMatch)(const TGenotype &Geno, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _PrepHaploMatch_def LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME' #define SIMD_NAME(NAME) NAME ## _avx ^ :297:1: note: expanded from here _PrepHaploMatch_avx ^ ./LibHLA.h:416:15: note: '_PrepHaploMatch_def' declared here static void _PrepHaploMatch_def(const TGenotype &pG, ^ LibHLA_ext_avx.cpp:536:10: error: out-of-line definition of '_BestGuess_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_BestGuess_def'? THLAType SIMD_NAME(CAlg_Prediction::_BestGuess)(const CHaplotypeList &Haplo, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _BestGuess_def LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME' #define SIMD_NAME(NAME) NAME ## _avx ^ :298:1: note: expanded from here _BestGuess_avx ^ ./LibHLA.h:421:19: note: '_BestGuess_def' declared here static THLAType _BestGuess_def(const CHaplotypeList &Haplo, const TGenotype &Geno); ^ LibHLA_ext_avx.cpp:542:8: error: out-of-line definition of '_PostProb_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_PostProb_def'? double SIMD_NAME(CAlg_Prediction::_PostProb)(const CHaplotypeList &Haplo, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _PostProb_def LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME' #define SIMD_NAME(NAME) NAME ## _avx ^ :299:1: note: expanded from here _PostProb_avx ^ ./LibHLA.h:424:17: note: '_PostProb_def' declared here static double _PostProb_def(const CHaplotypeList &Haplo, const TGenotype &Geno, const THLAType &HLA); ^ LibHLA_ext_avx.cpp:548:8: error: out-of-line definition of '_PostProb2_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_PostProb2_def'? double SIMD_NAME(CAlg_Prediction::_PostProb2)(const CHaplotypeList &Haplo, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _PostProb2_def LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME' #define SIMD_NAME(NAME) NAME ## _avx ^ :300:1: note: expanded from here _PostProb2_avx ^ ./LibHLA.h:427:17: note: '_PostProb2_def' declared here static double _PostProb2_def(const CHaplotypeList &Haplo, const TGenotype &Geno, double Prob[]); ^ 4 errors generated. make: *** [LibHLA_ext_avx.o] Error 1 ERROR: compilation failed for package ‘HIBAG’ * removing ‘/private/tmp/Rtmp9v0TIb/Rinstb977527b1269/HIBAG’ ----------------------------------- ERROR: package installation failed