* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’ * installing *source* package ‘outbreaker2’ ... ** package ‘outbreaker2’ 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 '/home/hornik/tmp/scratch/RtmpyCLERH/R.INSTALL210c64321a8c68/outbreaker2/src' g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c internals.cpp -o internals.o internals.cpp: In function ‘Rcpp::IntegerVector cpp_find_descendents(Rcpp::IntegerVector, size_t)’: internals.cpp:114:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 114 | for (size_t j = 0; j < alpha.size(); j++) { | ~~^~~~~~~~~~~~~~ internals.cpp:115:18: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | if (alpha[j] == i) n++; internals.cpp:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 121 | for (size_t j = 0; j < alpha.size(); j++) { | ~~^~~~~~~~~~~~~~ internals.cpp:122:18: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 122 | if (alpha[j] == i) { internals.cpp: In function ‘Rcpp::IntegerVector cpp_find_local_cases(Rcpp::IntegerVector, size_t)’: internals.cpp:169:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 169 | for (size_t j = 0; j < desc_i.size(); j++) { | ~~^~~~~~~~~~~~~~~ internals.cpp:178:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 178 | for (size_t j = 0; j < desc_alpha_i.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ internals.cpp:179:28: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 179 | if ( desc_alpha_i[j] != i) { internals.cpp: In function ‘Rcpp::List cpp_swap_cases(Rcpp::List, size_t)’: internals.cpp:251:21: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 251 | if (alpha_in[j] == i) { internals.cpp:253:28: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 253 | } else if (alpha_in[j] == x) { g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c likelihoods.cpp -o likelihoods.o likelihoods.cpp: In function ‘double cpp_ll_genetic(Rcpp::List, Rcpp::List, SEXP, Rcpp::RObject)’: likelihoods.cpp:114:40: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | if (kappa[j] < 1 || kappa[j] > K) { likelihoods.cpp:146:40: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 146 | if (kappa[j] < 1 || kappa[j] > K) { likelihoods.cpp: In function ‘double cpp_ll_timing_infections(Rcpp::List, Rcpp::List, SEXP, Rcpp::RObject)’: likelihoods.cpp:225:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 225 | if (delay < 1 || delay > w_dens.ncol()) { | ~~~~~~^~~~~~~~~~~~~~~ likelihoods.cpp:228:40: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 228 | if (kappa[j] < 1 || kappa[j] > K) { likelihoods.cpp:243:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 243 | if (delay < 1 || delay > w_dens.ncol()) { | ~~~~~~^~~~~~~~~~~~~~~ likelihoods.cpp:246:40: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 246 | if (kappa[j] < 1 || kappa[j] > K) { likelihoods.cpp: In function ‘double cpp_ll_timing_sampling(Rcpp::List, Rcpp::List, SEXP, Rcpp::RObject)’: likelihoods.cpp:304:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 304 | if (delay < 1 || delay > f_dens.size()) { | ~~~~~~^~~~~~~~~~~~~~~ likelihoods.cpp:316:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 316 | if (delay < 1 || delay > f_dens.size()) { | ~~~~~~^~~~~~~~~~~~~~~ likelihoods.cpp: In function ‘double cpp_ll_reporting(Rcpp::List, Rcpp::List, SEXP, Rcpp::RObject)’: likelihoods.cpp:384:40: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 384 | if (kappa[j] < 1 || kappa[j] > K) { likelihoods.cpp:397:40: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 397 | if (kappa[j] < 1 || kappa[j] > K) { g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c moves.cpp -o moves.o moves.cpp: In function ‘Rcpp::List cpp_move_kappa(Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::RObject)’: moves.cpp:566:44: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 566 | if (new_kappa[i] < 1 || new_kappa[i] > K) { g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c priors.cpp -o priors.o g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o outbreaker2.so RcppExports.o internals.o likelihoods.o moves.o priors.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpyCLERH/R.INSTALL210c64321a8c68/outbreaker2/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpyCLERH/R.INSTALL210c64321a8c68/outbreaker2/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpyCLERH/R.INSTALL210c64321a8c68/outbreaker2/src' installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-outbreaker2/00new/outbreaker2/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 ‘outbreaker2’ as ‘outbreaker2_1.1.3_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (outbreaker2)