* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rubias’ ...
** package ‘rubias’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpEm0Out/R.INSTALL39e57646981824/rubias/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_close_matchers.cpp -o rcpp_close_matchers.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_fullBayes_mcmc.cpp -o rcpp_fullBayes_mcmc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_gprobs.cpp -o rcpp_gprobs.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_indiv_specific_logl_means_and_vars.cpp -o rcpp_indiv_specific_logl_means_and_vars.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_per_locus_logls.cpp -o rcpp_per_locus_logls.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_sampling.cpp -o rcpp_sampling.o
rcpp_sampling.cpp: In function ‘Rcpp::IntegerVector samp_from_mat(Rcpp::NumericMatrix)’:
rcpp_sampling.cpp:38:12: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized]
38 | out[c] = res;
rcpp_sampling.cpp:21:12: note: ‘res’ was declared here
21 | int r,c, res;
| ^~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_simulation.cpp -o rcpp_simulation.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simple_pi_em.cpp -o simple_pi_em.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simple_pi_mcmc.cpp -o simple_pi_mcmc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c utilities.cpp -o utilities.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rubias.so RcppExports.o rcpp_close_matchers.o rcpp_fullBayes_mcmc.o rcpp_gprobs.o rcpp_indiv_specific_logl_means_and_vars.o rcpp_per_locus_logls.o rcpp_sampling.o rcpp_simulation.o simple_pi_em.o simple_pi_mcmc.o utilities.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpEm0Out/R.INSTALL39e57646981824/rubias/src'
make[1]: Entering directory '/tmp/RtmpEm0Out/R.INSTALL39e57646981824/rubias/src'
make[1]: Leaving directory '/tmp/RtmpEm0Out/R.INSTALL39e57646981824/rubias/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rubias/00new/rubias/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘rubias’
finding HTML links ... done
Hasselman_sim_colls html
a_freq_list html
alewife html
allelic_list html
assess_pb_bias_correction html
assess_reference_loo html
assess_reference_mc html
avg_coll2correctRU html
blueback html
bootstrap_rho html
check_known_collections html
check_refmix html
chinook html
chinook_collection_levels html
chinook_mix html
chinook_repunit_levels html
close_matching_samples html
count_missing_data html
custom_pi_prior html
dirch_from_allocations html
dirch_from_counts html
geno_logL html
geno_logL_ssq html
get_ploidy_from_frame html
gprob_sim_gc html
gprob_sim_gc_missing html
gprob_sim_ind html
gsi_em_1 html
gsi_mcmc_1 html
gsi_mcmc_fb html
infer_mixture html
list_diploid_params html
mixture_draw html
modify_scaled_likelihoods_for_known_mixture_fish
html
per_locus_means_and_vars html
perfect_chinook html
perfect_chinook_mix html
pipe html
rcpp_close_matchers html
rcpp_indiv_specific_logl_means_and_vars
html
rcpp_per_locus_logls html
read_gsi_sim html
ref_and_mix_pipeline html
reference_allele_counts html
round2 html
rubias html
samp_from_mat html
self_assign html
sim_spec_examples html
simulate_random_samples html
small_chinook_mix html
small_chinook_ref html
tcf2long html
tcf2param_list html
tidy_mcmc_coll_rep_stuff html
tidy_mcmc_pofz html
tidy_pi_traces html
write_gsi_sim_mixture html
write_gsi_sim_reference html
** 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 (rubias)