* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * 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-18 accepts -g... yes checking for clang-18 option to enable C11 features... none needed checking for gsl-config... /usr/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: ‘Debian clang version 18.1.4 (1)’ make[1]: Entering directory '/tmp/Rtmpo96KIN/R.INSTALL356038797a11f6/island/src' clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Checking_for_Parameter_Correctness.c -o Checking_for_Parameter_Correctness.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Counting_Replicates_per_Time.c -o Counting_Replicates_per_Time.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Counting_Type_of_Transitions.c -o Counting_Type_of_Transitions.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Create_Binary_Combination.c -o Create_Binary_Combination.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c EUCLIDIAN_DISTANCE_MATRIX.c -o EUCLIDIAN_DISTANCE_MATRIX.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c GSL_MacKenzie_NLL_Uneven_Function.c -o GSL_MacKenzie_NLL_Uneven_Function.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c GSL_MacKenzie_NLLikelihood_Function.c -o GSL_MacKenzie_NLLikelihood_Function.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c GSL_Minimization_Simplex.c -o GSL_Minimization_Simplex.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c GSL_NLL_Function_Uneven.c -o GSL_NLL_Function_Uneven.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c GSL_NLLikelihood_Function.c -o GSL_NLLikelihood_Function.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c IO_AKAIKE_Model_Selection.c -o IO_AKAIKE_Model_Selection.o IO_AKAIKE_Model_Selection.c:56:11: warning: unused variable 'p' [-Wunused-variable] 56 | char * p; | ^ 1 warning generated. clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c IO_Missing_Values.c -o IO_Missing_Values.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c -o MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.o MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:57:13: warning: unused variable 'l' [-Wunused-variable] 57 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:57:15: warning: unused variable 's' [-Wunused-variable] 57 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:154:13: warning: unused variable 'l' [-Wunused-variable] 154 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:154:15: warning: unused variable 's' [-Wunused-variable] 154 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c:154:19: warning: unused variable 'n' [-Wunused-variable] 154 | 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] 290 | double Total_NLL_Value = 0.0; | ^ 6 warnings generated. clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.c -o MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c MODEL_SELECTION_UPGMA_R_FUNCTION.c -o MODEL_SELECTION_UPGMA_R_FUNCTION.o MODEL_SELECTION_UPGMA_R_FUNCTION.c:35:13: warning: unused variable 'l' [-Wunused-variable] 35 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:35:15: warning: unused variable 's' [-Wunused-variable] 35 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:123:13: warning: unused variable 'l' [-Wunused-variable] 123 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:123:15: warning: unused variable 's' [-Wunused-variable] 123 | int i,j,k,l,s, n; | ^ MODEL_SELECTION_UPGMA_R_FUNCTION.c:123:19: warning: unused variable 'n' [-Wunused-variable] 123 | 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] 195 | double Total_NLL_Value = 0.0; | ^ 6 warnings generated. clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c MODEL_SELECTION_UPGMA_R_SHLIB.c -o MODEL_SELECTION_UPGMA_R_SHLIB.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c MacKenzie_NLLikelihood_Function.c -o MacKenzie_NLLikelihood_Function.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Parameter_Model.c -o Parameter_Model.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Parameter_Space_R_SHLIB.c -o Parameter_Space_R_SHLIB.o Parameter_Space_R_SHLIB.c:59:10: warning: unused variable 'j' [-Wunused-variable] 59 | int i, j, key; | ^ 1 warning generated. clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Probability_Rates.c -o Probability_Rates.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c -o R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.o R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:14:13: warning: unused variable 'l' [-Wunused-variable] 14 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:14:15: warning: unused variable 's' [-Wunused-variable] 14 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:80:13: warning: unused variable 'l' [-Wunused-variable] 80 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:80:15: warning: unused variable 's' [-Wunused-variable] 80 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c:80:19: warning: unused variable 'n' [-Wunused-variable] 80 | int i,j,k,l,s, n; | ^ 5 warnings generated. clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.c -o R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.o R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.c:76:7: warning: unused variable 'i' [-Wunused-variable] 76 | int i,j,k,m; | ^ 1 warning generated. clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c R_SHLIB___mle_NLL_Uneven_Minimization.c -o R_SHLIB___mle_NLL_Uneven_Minimization.o R_SHLIB___mle_NLL_Uneven_Minimization.c:70:13: warning: unused variable 'l' [-Wunused-variable] 70 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:70:15: warning: unused variable 's' [-Wunused-variable] 70 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:151:13: warning: unused variable 'l' [-Wunused-variable] 151 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:151:15: warning: unused variable 's' [-Wunused-variable] 151 | int i,j,k,l,s, n; | ^ R_SHLIB___mle_NLL_Uneven_Minimization.c:151:19: warning: unused variable 'n' [-Wunused-variable] 151 | int i,j,k,l,s, n; | ^ 5 warnings generated. clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Rates_into_Probabilities.c -o Rates_into_Probabilities.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c SP_Matrix_Data.c -o SP_Matrix_Data.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Time_Control.c -o Time_Control.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c Transition_Matrix.c -o Transition_Matrix.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c UPGMA_CLUSTERING_PARTITION.c -o UPGMA_CLUSTERING_PARTITION.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c init.c -o init.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c mle_Col_Ext_Uneven_Matrix_R_SHLIB.c -o mle_Col_Ext_Uneven_Matrix_R_SHLIB.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c mle_MacKenzie_Uneven_Matrix_R_SHLIB.c -o mle_MacKenzie_Uneven_Matrix_R_SHLIB.o clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I/usr/include -I./ -I/usr/local/include -D_FORTIFY_SOURCE=3 -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -g -O3 -Wall -pedantic -c upgma_clustering.c -o upgma_clustering.o clang-18 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/tmp/Rtmpo96KIN/R.INSTALL356038797a11f6/island/src' make[1]: Entering directory '/tmp/Rtmpo96KIN/R.INSTALL356038797a11f6/island/src' make[1]: Leaving directory '/tmp/Rtmpo96KIN/R.INSTALL356038797a11f6/island/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-island/00new/island/libs ** 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 * creating tarball packaged installation of ‘island’ as ‘island_0.2.10_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (island)