* installing *source* package ‘poppr’ ...
** this is package ‘poppr’ version ‘2.9.8’
** package ‘poppr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 21.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/poppr/src'
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c adjust_missing.c -o adjust_missing.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c bitwise_distance.c -o bitwise_distance.o
bitwise_distance.c:815:7: warning: variable 'chr_length' set but not used [-Wunused-but-set-variable]
  815 |   int chr_length;
      |       ^
bitwise_distance.c:1190:7: warning: variable 'chr_length' set but not used [-Wunused-but-set-variable]
 1190 |   int chr_length;
      |       ^
2 warnings generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c init.c -o init.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c mlg_clustering.c -o mlg_clustering.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c mlg_counter.c -o mlg_counter.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c msn.c -o msn.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c omp_test.c -o omp_test.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c permut_shuffler.c -o permut_shuffler.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang21/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c poppr_distance.c -o poppr_distance.o
poppr_distance.c:428:6: warning: variable 'numel' set but not used [-Wunused-but-set-variable]
  428 |         int numel; // Number of elements in returned matrix
      |             ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o poppr.so adjust_missing.o bitwise_distance.o init.o mlg_clustering.o mlg_counter.o msn.o omp_test.o permut_shuffler.o poppr_distance.o -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/poppr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/poppr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/poppr/src'
installing to /data/gannet/ripley/R/packages/tests-clang/poppr.Rcheck/00LOCK-poppr/00new/poppr/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘as.genambig’ in package ‘poppr’
** help
*** installing help indices
*** copying figures
** 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 (poppr)