* installing to library ‘/home/hornik/tmp/R.check/r-patched-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 '/tmp/RtmpLfQSXQ/R.INSTALL1425b17f268ffc/poppr/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpLfQSXQ/R.INSTALL1425b17f268ffc/poppr/src'
make[1]: Entering directory '/tmp/RtmpLfQSXQ/R.INSTALL1425b17f268ffc/poppr/src'
make[1]: Leaving directory '/tmp/RtmpLfQSXQ/R.INSTALL1425b17f268ffc/poppr/src'
installing to /home/hornik/tmp/R.check/r-patched-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
converting help for package ‘poppr’
finding HTML links ... done
Aeut html
MLG-accessors html
finding level-2 HTML links ... done
MLG-class html
MLG-method html
Pinf html
Pram html
aboot html
bitwise.dist html
bitwise.ia html
boot.ia html
bootgen-class html
bootgen-methods html
bruvo.boot html
bruvo.dist html
bruvo.msn html
bruvomat-class html
bruvomat-methods html
clonecorrect html
coercion-methods html
cutoff_predictor html
diss.dist html
diversity_boot html
diversity_ci html
diversity_stats html
filter_stats html
fix_replen html
genclone-class html
genclone-method html
genetic_distance html
genind2genalex html
genotype_curve html
getfile html
grapes-greater-than-grapes html
greycurve html
ia html
imsn html
incomp html
info_table html
informloci html
is.clone html
levels-methods html
locus_table html
make_haplotypes-method html
missingno html
mlg html
mlg.filter html
mll-method html
mll.custom html
mll.reset-method html
monpop html
old2new_genclone html
partial_clone html
pgen html
plot_filter_stats html
plot_poppr_msn html
poppr-package html
poppr html
poppr.all html
poppr.amova html
poppr.msn html
poppr.plot html
poppr_has_parallel html
popsub html
private_alleles html
psex html
rare_allele_correction html
read.genalex html
recode_polyploids html
rraf html
rrmlg html
samp.ia html
shufflepop html
snpclone-coercion-methods html
snpclone-method html
test_replen html
unique-methods html
upgma html
win.ia html
*** 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)