* installing *source* package ‘outbreaker2’ ...
** package ‘outbreaker2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/outbreaker2/src'
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -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++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c likelihoods.cpp -o likelihoods.o
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -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) {
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++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c priors.cpp -o priors.o
g++-14 -std=gnu++11 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o outbreaker2.so RcppExports.o internals.o likelihoods.o moves.o priors.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/outbreaker2/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/outbreaker2/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/outbreaker2/src'
installing to /data/gannet/ripley/R/packages/tests-devel/outbreaker2.Rcheck/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
* DONE (outbreaker2)