* installing *source* package 'outbreaker2' ...
** this is package 'outbreaker2' version '1.1.3'
** package 'outbreaker2' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 14.2.0'
using C++11
make[1]: Entering directory '/d/temp/2025_10_21_12_47_29_10822/RtmpiER3TF/R.INSTALL58b0430d7033/outbreaker2/src'
g++  -std=gnu++11 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -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++11 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -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:225:34: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long 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 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 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 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 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 long unsigned int'} [-Wsign-compare]
  397 |           if (kappa[j] < 1 || kappa[j] > K) {
g++  -std=gnu++11 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -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++11 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c priors.cpp -o priors.o
g++ -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-4.5.1/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_10_21_12_47_29_10822/RtmpiER3TF/R.INSTALL58b0430d7033/outbreaker2/src'
make[1]: Entering directory '/d/temp/2025_10_21_12_47_29_10822/RtmpiER3TF/R.INSTALL58b0430d7033/outbreaker2/src'
make[1]: Leaving directory '/d/temp/2025_10_21_12_47_29_10822/RtmpiER3TF/R.INSTALL58b0430d7033/outbreaker2/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-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
* MD5 sums
packaged installation of 'outbreaker2' as outbreaker2_1.1.3.zip
* DONE (outbreaker2)