* installing *source* package ‘island’ ... ** package ‘island’ 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 the compiler supports GNU C... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to enable C11 features... none needed checking for gsl-config... /opt/R/x86_64/bin/gsl-config checking if GSL version >= 1.15... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h config.status: src/config.h is unchanged ** libs using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Checking_for_Parameter_Correctness.c -o Checking_for_Parameter_Correctness.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Counting_Replicates_per_Time.c -o Counting_Replicates_per_Time.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Counting_Type_of_Transitions.c -o Counting_Type_of_Transitions.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Create_Binary_Combination.c -o Create_Binary_Combination.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c EUCLIDIAN_DISTANCE_MATRIX.c -o EUCLIDIAN_DISTANCE_MATRIX.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c GSL_MacKenzie_NLL_Uneven_Function.c -o GSL_MacKenzie_NLL_Uneven_Function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c GSL_MacKenzie_NLLikelihood_Function.c -o GSL_MacKenzie_NLLikelihood_Function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c GSL_Minimization_Simplex.c -o GSL_Minimization_Simplex.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c GSL_NLL_Function_Uneven.c -o GSL_NLL_Function_Uneven.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c GSL_NLLikelihood_Function.c -o GSL_NLLikelihood_Function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c IO_AKAIKE_Model_Selection.c -o IO_AKAIKE_Model_Selection.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c IO_Missing_Values.c -o IO_Missing_Values.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c -o MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.c -o MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.o IO_AKAIKE_Model_Selection.c:56:11: warning: unused variable 'p' [-Wunused-variable] char * p; ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c MODEL_SELECTION_UPGMA_R_FUNCTION.c -o MODEL_SELECTION_UPGMA_R_FUNCTION.o MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:57:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:57:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:154:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:154:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:154:19: warning: unused variable 'n' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:290:10: warning: variable 'Total_NLL_Value' set but not used [-Wunused-but-set-variable] double Total_NLL_Value = 0.0; ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c MODEL_SELECTION_UPGMA_R_SHLIB.c -o MODEL_SELECTION_UPGMA_R_SHLIB.o MODEL_SELECTION_UPGMA_R_FUNCTION.c:35:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:35:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:123:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:123:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:123:19: warning: unused variable 'n' [-Wunused-variable] int i,j,k,l,s, n; ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:195:10: warning: variable 'Total_NLL_Value' set but not used [-Wunused-but-set-variable] double Total_NLL_Value = 0.0; ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c MacKenzie_NLLikelihood_Function.c -o MacKenzie_NLLikelihood_Function.o 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Parameter_Model.c -o Parameter_Model.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Parameter_Space_R_SHLIB.c -o Parameter_Space_R_SHLIB.o 6 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Probability_Rates.c -o Probability_Rates.o 6 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c -o R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.o Parameter_Space_R_SHLIB.c:59:10: warning: unused variable 'j' [-Wunused-variable] int i, j, key; ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.c -o R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c R_SHLIB___mle_NLL_Uneven_Minimization.c -o R_SHLIB___mle_NLL_Uneven_Minimization.o 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Rates_into_Probabilities.c -o Rates_into_Probabilities.o R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:14:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:14:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:80:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:80:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:80:19: warning: unused variable 'n' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:70:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:70:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:151:13: warning: unused variable 'l' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:151:15: warning: unused variable 's' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:151:19: warning: unused variable 'n' [-Wunused-variable] int i,j,k,l,s, n; ^ R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.c:76:7: warning: unused variable 'i' [-Wunused-variable] int i,j,k,m; ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c SP_Matrix_Data.c -o SP_Matrix_Data.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Time_Control.c -o Time_Control.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c Transition_Matrix.c -o Transition_Matrix.o 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c UPGMA_CLUSTERING_PARTITION.c -o UPGMA_CLUSTERING_PARTITION.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c mle_Col_Ext_Uneven_Matrix_R_SHLIB.c -o mle_Col_Ext_Uneven_Matrix_R_SHLIB.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c mle_MacKenzie_Uneven_Matrix_R_SHLIB.c -o mle_MacKenzie_Uneven_Matrix_R_SHLIB.o 5 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -I./ -I/opt/R/x86_64/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fPIC -falign-functions=64 -Wall -g -O2 -c upgma_clustering.c -o upgma_clustering.o 5 warnings generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o island.so Checking_for_Parameter_Correctness.o Counting_Replicates_per_Time.o Counting_Type_of_Transitions.o Create_Binary_Combination.o EUCLIDIAN_DISTANCE_MATRIX.o GSL_MacKenzie_NLL_Uneven_Function.o GSL_MacKenzie_NLLikelihood_Function.o GSL_Minimization_Simplex.o GSL_NLL_Function_Uneven.o GSL_NLLikelihood_Function.o IO_AKAIKE_Model_Selection.o IO_Missing_Values.o MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.o MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.o MODEL_SELECTION_UPGMA_R_FUNCTION.o MODEL_SELECTION_UPGMA_R_SHLIB.o MacKenzie_NLLikelihood_Function.o Parameter_Model.o Parameter_Space_R_SHLIB.o Probability_Rates.o R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.o R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.o R_SHLIB___mle_NLL_Uneven_Minimization.o Rates_into_Probabilities.o SP_Matrix_Data.o Time_Control.o Transition_Matrix.o UPGMA_CLUSTERING_PARTITION.o init.o mle_Col_Ext_Uneven_Matrix_R_SHLIB.o mle_MacKenzie_Uneven_Matrix_R_SHLIB.o upgma_clustering.o -L./ -L/opt/R/x86_64/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/island.Rcheck/00LOCK-island/00new/island/libs ** generating debug symbols (dSYM) ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (island)