* 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 /usr/local/clang18/bin/clang accepts -g... yes
checking for /usr/local/clang18/bin/clang 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: ‘clang version 18.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/island/src'
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Checking_for_Parameter_Correctness.c -o Checking_for_Parameter_Correctness.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Counting_Replicates_per_Time.c -o Counting_Replicates_per_Time.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Counting_Type_of_Transitions.c -o Counting_Type_of_Transitions.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Create_Binary_Combination.c -o Create_Binary_Combination.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c EUCLIDIAN_DISTANCE_MATRIX.c -o EUCLIDIAN_DISTANCE_MATRIX.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c GSL_MacKenzie_NLL_Uneven_Function.c -o GSL_MacKenzie_NLL_Uneven_Function.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c GSL_MacKenzie_NLLikelihood_Function.c -o GSL_MacKenzie_NLLikelihood_Function.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c GSL_Minimization_Simplex.c -o GSL_Minimization_Simplex.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c GSL_NLL_Function_Uneven.c -o GSL_NLL_Function_Uneven.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c GSL_NLLikelihood_Function.c -o GSL_NLLikelihood_Function.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c IO_Missing_Values.c -o IO_Missing_Values.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.c -o MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c MODEL_SELECTION_UPGMA_R_SHLIB.c -o MODEL_SELECTION_UPGMA_R_SHLIB.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c MacKenzie_NLLikelihood_Function.c -o MacKenzie_NLLikelihood_Function.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Parameter_Model.c -o Parameter_Model.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Probability_Rates.c -o Probability_Rates.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -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.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Rates_into_Probabilities.c -o Rates_into_Probabilities.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c SP_Matrix_Data.c -o SP_Matrix_Data.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Time_Control.c -o Time_Control.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Transition_Matrix.c -o Transition_Matrix.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c UPGMA_CLUSTERING_PARTITION.c -o UPGMA_CLUSTERING_PARTITION.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c mle_Col_Ext_Uneven_Matrix_R_SHLIB.c -o mle_Col_Ext_Uneven_Matrix_R_SHLIB.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c mle_MacKenzie_Uneven_Matrix_R_SHLIB.c -o mle_MacKenzie_Uneven_Matrix_R_SHLIB.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I/usr/include -I./ -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNON_CPGPLOT_REPRESENTATION -DR_SHLIB -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c upgma_clustering.c -o upgma_clustering.o
/usr/local/clang18/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -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./ -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/island/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/island/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/island/src'
installing to /data/gannet/ripley/R/packages/tests-clang/island.Rcheck/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
* DONE (island)