* installing *source* package 'SITH' ... ** package 'SITH' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 13.3.0' make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpUTD6tz/R.INSTALL18b08794df6/SITH/src' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/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-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 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 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 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 long unsigned int'} [-Wsign-compare] 338 | for(int i = 0; i < v.size(); ++i) { | ~~^~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.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 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 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 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 long unsigned int'} [-Wsign-compare] 72 | for(int j = i+1; j < a.size(); ++j) { | ~~^~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c postproc.cpp -o postproc.o 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 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 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 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 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 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 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 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 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 long unsigned int'} [-Wsign-compare] 42 | for(int i = 1; i < species.size(); ++i) { | ~~^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulations.cpp -o simulations.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 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 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 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 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 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 long unsigned int'} and 'int' [-Wsign-compare] 105 | while(cells.size() < tumor_size) | ~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simutils.cpp -o simutils.o 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 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 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 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 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 long unsigned int'} [-Wsign-compare] 161 | for(int i = 0; i < v.size(); ++i) { | ~~^~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o SITH.dll tmp.def RcppExports.o gillespie.o main.o postproc.o simulations.o simutils.o -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.2/bin/x64 -lR make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/RtmpUTD6tz/R.INSTALL18b08794df6/SITH/src' make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpUTD6tz/R.INSTALL18b08794df6/SITH/src' make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/RtmpUTD6tz/R.INSTALL18b08794df6/SITH/src' installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-SITH/00new/SITH/libs/x64 ** 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 ** 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 'SITH' as SITH_1.1.0.zip * DONE (SITH)