* installing *source* package ‘poppr’ ...
** package ‘poppr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/poppr/src'
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c adjust_missing.c -o adjust_missing.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bitwise_distance.c -o bitwise_distance.o
bitwise_distance.c: In function ‘association_index_haploid’:
bitwise_distance.c:823:7: warning: unused variable ‘only_differences’ [-Wunused-variable]
  823 |   int only_differences;
      |       ^~~~~~~~~~~~~~~~
bitwise_distance.c:815:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable]
  815 |   int chr_length;
      |       ^~~~~~~~~~
bitwise_distance.c:808:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable]
  808 |   SEXP R_chr2_1;
      |        ^~~~~~~~
bitwise_distance.c: In function ‘association_index_diploid’:
bitwise_distance.c:1190:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable]
 1190 |   int chr_length;
      |       ^~~~~~~~~~
bitwise_distance.c:1182:8: warning: unused variable ‘R_chr2_2’ [-Wunused-variable]
 1182 |   SEXP R_chr2_2;
      |        ^~~~~~~~
bitwise_distance.c:1181:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable]
 1181 |   SEXP R_chr2_1;
      |        ^~~~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c init.c -o init.o
init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   24 | extern SEXP omp_test();
      | ^~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c mlg_clustering.c -o mlg_clustering.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c mlg_counter.c -o mlg_counter.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c msn.c -o msn.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c omp_test.c -o omp_test.o
omp_test.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
    7 | SEXP omp_test()
      |      ^~~~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c permut_shuffler.c -o permut_shuffler.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c poppr_distance.c -o poppr_distance.o
poppr_distance.c: In function ‘bruvo_between’:
poppr_distance.c:428:13: warning: variable ‘numel’ set but not used [-Wunused-but-set-variable]
  428 |         int numel; // Number of elements in returned matrix
      |             ^~~~~
gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -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-devel/poppr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/poppr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/poppr/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)