* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘scanstatistics’ ...
** package ‘scanstatistics’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmptFg4St/R.INSTALL1480a21933b563/scanstatistics/src'
g++-13 -std=gnu++11 -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/RcppArmadillo/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++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c probability_functions.cpp -o probability_functions.o
probability_functions.cpp: In function ‘double poisson_loglihood(const arma::uvec&, const arma::vec&, double)’:
probability_functions.cpp:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
33 | for (int i = 0; i < y.n_elem; ++i) {
| ~~^~~~~~~~~~
probability_functions.cpp: In function ‘double zip_loglihood(const arma::uvec&, const arma::vec&, const arma::vec&, double)’:
probability_functions.cpp:86:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
86 | for (int i = 0; i < y.n_elem; ++i) {
| ~~^~~~~~~~~~
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scan_bayes_negbin.cpp -o scan_bayes_negbin.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scan_eb_negbin.cpp -o scan_eb_negbin.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scan_eb_poisson.cpp -o scan_eb_poisson.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scan_eb_zip.cpp -o scan_eb_zip.o
In file included from scan_eb_zip.cpp:2:
EBZIPscan.h: In member function ‘virtual void EBZIPscan::calculate(arma::uword, arma::uword, arma::uword, const arma::uvec&, const arma::uvec&)’:
EBZIPscan.h:132:17: warning: ‘loglik_new’ may be used uninitialized [-Wmaybe-uninitialized]
132 | (this->*store)(storage_index, loglik_new - loglik_null, q_hat, n_iterations,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
133 | zone_nr + 1, duration + 1);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
EBZIPscan.h:106:10: note: ‘loglik_new’ was declared here
106 | double loglik_new;
| ^~~~~~~~~~
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scan_pb_perm.cpp -o scan_pb_perm.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scan_pb_poisson.cpp -o scan_pb_poisson.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scan_utility.cpp -o scan_utility.o
scan_utility.cpp: In function ‘arma::uvec shuffle_time_counts(const arma::uvec&)’:
scan_utility.cpp:69:42: warning: comparison of integer expressions of different signedness: ‘arma::sword’ {aka ‘int’} and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
69 | for (arma::uword i = res.n_elem - 1; k < res.n_elem; --i, ++k) {
| ~~^~~~~~~~~~~~
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o scanstatistics.so RcppExports.o probability_functions.o scan_bayes_negbin.o scan_eb_negbin.o scan_eb_poisson.o scan_eb_zip.o scan_pb_perm.o scan_pb_poisson.o scan_utility.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmptFg4St/R.INSTALL1480a21933b563/scanstatistics/src'
make[1]: Entering directory '/tmp/RtmptFg4St/R.INSTALL1480a21933b563/scanstatistics/src'
make[1]: Leaving directory '/tmp/RtmptFg4St/R.INSTALL1480a21933b563/scanstatistics/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-scanstatistics/00new/scanstatistics/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 ‘scanstatistics’
finding HTML links ... done
NM_geo html
NM_map html
NM_popcas html
closest_subsets html
connected_neighbors html
connected_to html
coords_to_knn html
df_to_matrix html
dist_to_knn html
estimate_baselines html
estimate_variances html
estimate_zip_params html
flexible_zones html
flipud html
get_zero_indices html
get_zone html
gumbel_pvalue html
has_converged html
if_connected html
is_connected html
knn_zones html
matrix_to_df html
mc_pvalue html
permute_matrix html
powerset_zones html
print.scanstatistic html
run_scan html
scan_bayes_negbin html
scan_bayes_negbin_cpp html
scan_eb_negbin html
scan_eb_negbin_cpp html
scan_eb_poisson html
scan_eb_poisson_cpp html
scan_eb_zip html
scan_eb_zip_cpp html
scan_pb_perm_cpp html
scan_pb_poisson html
scan_pb_poisson_cpp html
scan_permutation html
scanstatistics html
score_locations html
top_clusters 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 (scanstatistics)