* installing *source* package 'outbreaker2' ... ** this is package 'outbreaker2' version '1.1.4' ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 14.3.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 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 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 long unsigned int'} [-Wsign-compare] 253 | } else if (alpha_in[j] == x) { g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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:240:40: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] 240 | if (kappa[j] < 1 || kappa[j] > K) { likelihoods.cpp:264:40: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] 264 | 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:322:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 322 | if (delay < 1 || delay > f_dens.size()) { | ~~~~~~^~~~~~~~~~~~~~~ likelihoods.cpp:334:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 334 | if (delay < 1 || delay > f_dens.size()) { | ~~~~~~^~~~~~~~~~~~~~~ likelihoods.cpp: In function 'double cpp_ll_reporting(Rcpp::List, Rcpp::List, SEXP, Rcpp::RObject)': likelihoods.cpp:402:40: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] 402 | if (kappa[j] < 1 || kappa[j] > K) { likelihoods.cpp:415:40: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] 415 | if (kappa[j] < 1 || kappa[j] > K) { g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare] 566 | if (new_kappa[i] < 1 || new_kappa[i] > K) { g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c priors.cpp -o priors.o g++ -std=gnu++17 -shared -s -static-libgcc -o outbreaker2.dll tmp.def RcppExports.o internals.o likelihoods.o moves.o priors.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-outbreaker2/00new/outbreaker2/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (outbreaker2)