* installing *source* package 'poppr' ...
** package 'poppr' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2024_12_22_01_50_00_26287/Rtmpew2kwo/R.INSTALL2b6c01e84120a/poppr/src'
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c adjust_missing.c -o adjust_missing.o
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mlg_clustering.c -o mlg_clustering.o
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mlg_counter.c -o mlg_counter.o
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c msn.c -o msn.o
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c omp_test.c -o omp_test.o
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c permut_shuffler.c -o permut_shuffler.o
gcc -I"D:/RCompile/recent/R/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -s -static-libgcc -o poppr.dll tmp.def 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 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_22_01_50_00_26287/Rtmpew2kwo/R.INSTALL2b6c01e84120a/poppr/src'
make[1]: Entering directory '/d/temp/2024_12_22_01_50_00_26287/Rtmpew2kwo/R.INSTALL2b6c01e84120a/poppr/src'
make[1]: Leaving directory '/d/temp/2024_12_22_01_50_00_26287/Rtmpew2kwo/R.INSTALL2b6c01e84120a/poppr/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-poppr/00new/poppr/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'poppr' as poppr_2.9.6.zip
* DONE (poppr)