* installing *source* package ‘SITH’ ...
** package ‘SITH’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/SITH/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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   -c gillespie.cpp -o gillespie.o
In file included from neighbors.h:10,
                 from gillespie.h:10,
                 from gillespie.cpp:1:
simutils.h: In function 'int max_mut(std::vector<specie>&)':
simutils.h:58:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   58 |     for(int i = 0; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |         if(species[i].genotype.size() > max) {
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function 'std::vector<int> bubblesort(std::vector<int>)':
simutils.h:71:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |     for(int i = 0; i < a.size(); ++i) {
      |                    ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   72 |         for(int j = i+1; j < a.size(); ++j) {
      |                          ~~^~~~~~~~~~
gillespie.cpp: In function 'cell birth_cellUDT(cell&, int, specie, std::vector<specie>&)':
gillespie.cpp:243:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Edge>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  243 |         for(int j = 0; j < G[*it].size(); ++j) {
      |                        ~~^~~~~~~~~~~~~~~
gillespie.cpp: In function 'int find_gtype(std::vector<specie>&, std::vector<int>)':
gillespie.cpp:329:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  329 |     for(int i = 0; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
gillespie.cpp: In function 'bool vin(std::vector<int>, int)':
gillespie.cpp:338:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  338 |     for(int i = 0; i < v.size(); ++i) {
      |                    ~~^~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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   -c main.cpp -o main.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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   -c postproc.cpp -o postproc.o
In file included from simulations.h:4,
                 from main.cpp:1:
simutils.h: In function 'int max_mut(std::vector<specie>&)':
simutils.h:58:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   58 |     for(int i = 0; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |         if(species[i].genotype.size() > max) {
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function 'std::vector<int> bubblesort(std::vector<int>)':
simutils.h:71:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |     for(int i = 0; i < a.size(); ++i) {
      |                    ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   72 |         for(int j = i+1; j < a.size(); ++j) {
      |                          ~~^~~~~~~~~~
In file included from postproc.h:4,
                 from postproc.cpp:1:
simutils.h: In function 'int max_mut(std::vector<specie>&)':
simutils.h:58:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   58 |     for(int i = 0; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |         if(species[i].genotype.size() > max) {
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function 'std::vector<int> bubblesort(std::vector<int>)':
simutils.h:71:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |     for(int i = 0; i < a.size(); ++i) {
      |                    ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   72 |         for(int j = i+1; j < a.size(); ++j) {
      |                          ~~^~~~~~~~~~
postproc.cpp: In function 'void PostProcessing::write_results(std::vector<cell>&, std::vector<specie>&, Rcpp::NumericMatrix&, Rcpp::IntegerMatrix&, Rcpp::IntegerVector&)':
postproc.cpp:6:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<cell>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
    6 |     for(int i = 0; i < cells.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~
postproc.cpp:17:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   17 |     for(int i = 0; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
postproc.cpp:19:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   19 |         for(int j = 0; j < species[i].genotype.size(); ++j) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
postproc.cpp: In function 'void PostProcessing::write_phylo_tree(std::vector<std::vector<int> >&, Rcpp::IntegerMatrix&)':
postproc.cpp:31:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   31 |     for(int i = 0; i < phylo_tree[0].size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~
postproc.cpp: In function 'Rcpp::NumericMatrix PostProcessing::get_color_scheme(std::vector<specie>&)':
postproc.cpp:42:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   42 |     for(int i = 1; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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   -c simulations.cpp -o simulations.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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   -c simutils.cpp -o simutils.o
In file included from simulations.h:4,
                 from simulations.cpp:1:
simutils.h: In function 'int max_mut(std::vector<specie>&)':
simutils.h:58:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   58 |     for(int i = 0; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |         if(species[i].genotype.size() > max) {
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function 'std::vector<int> bubblesort(std::vector<int>)':
simutils.h:71:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |     for(int i = 0; i < a.size(); ++i) {
      |                    ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   72 |         for(int j = i+1; j < a.size(); ++j) {
      |                          ~~^~~~~~~~~~
simulations.cpp: In function 'Rcpp::List Sims::simulateIA(Rcpp::List)':
simulations.cpp:30:24: warning: comparison of integer expressions of different signedness: 'std::vector<cell>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   30 |     while(cells.size() < tumor_size)
      |           ~~~~~~~~~~~~~^~~~~~~~~~~~
simulations.cpp: In function 'Rcpp::List Sims::simulateUDT(Rcpp::List)':
simulations.cpp:105:24: warning: comparison of integer expressions of different signedness: 'std::vector<cell>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  105 |     while(cells.size() < tumor_size)
      |           ~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from simutils.cpp:1:
simutils.h: In function 'int max_mut(std::vector<specie>&)':
simutils.h:58:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<specie>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   58 |     for(int i = 0; i < species.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
simutils.h:59:39: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   59 |         if(species[i].genotype.size() > max) {
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
simutils.h: In function 'std::vector<int> bubblesort(std::vector<int>)':
simutils.h:71:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |     for(int i = 0; i < a.size(); ++i) {
      |                    ~~^~~~~~~~~~
simutils.h:72:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   72 |         for(int j = i+1; j < a.size(); ++j) {
      |                          ~~^~~~~~~~~~
simutils.cpp: In function 'std::vector<std::vector<int> > get_perms(std::vector<int>)':
simutils.cpp:161:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  161 |         for(int i = 0; i < v.size(); ++i) {
      |                        ~~^~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o SITH.so RcppExports.o gillespie.o main.o postproc.o simulations.o simutils.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/SITH/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/SITH/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/SITH/src'
installing to /data/gannet/ripley/R/packages/tests-devel/SITH.Rcheck/00LOCK-SITH/00new/SITH/libs
** R
** 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 (SITH)