* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘poppr’ ...
** package ‘poppr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphbL1Rp/R.INSTALL213fe6430d3fc/poppr/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c adjust_missing.c -o adjust_missing.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -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-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c mlg_clustering.c -o mlg_clustering.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c mlg_counter.c -o mlg_counter.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msn.c -o msn.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c omp_test.c -o omp_test.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c permut_shuffler.c -o permut_shuffler.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -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-13 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -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 -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphbL1Rp/R.INSTALL213fe6430d3fc/poppr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphbL1Rp/R.INSTALL213fe6430d3fc/poppr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphbL1Rp/R.INSTALL213fe6430d3fc/poppr/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
* creating tarball
packaged installation of ‘poppr’ as ‘poppr_2.9.6_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (poppr)