* installing *source* package 'junctions' ...
** this is package 'junctions' version '2.1.3'
** package 'junctions' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 14.2.0'
using C++17
make[1]: Entering directory '/d/temp/2025_06_29_01_50_00_26597/RtmpAxbSfI/R.INSTALL2d3a06582719c/junctions/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/nloptr/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Fish.cpp -o Fish.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/nloptr/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Output.cpp -o Output.o
Output.cpp: In function 'std::vector<int> detect_ancestry(const std::vector<junction>&, const std::vector<double>&)':
Output.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<junction>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
102 | for (; j <= (G.size() - 1); ++j) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/nloptr/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -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/nloptr/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c backcrossing.cpp -o backcrossing.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/nloptr/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimate_time_unphased.cpp -o estimate_time_unphased.o
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb.h:32,
from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel/TBB.h:10,
from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel.h:24,
from estimate_time_unphased.cpp:22:
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/nloptr/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main_functions.cpp -o main_functions.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/nloptr/include' -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c unphased.cpp -o unphased.o
unphased.cpp: In function 'void update_pop(const std::vector<Fish_inf>&, std::vector<Fish_inf>*, int, double, size_t)':
unphased.cpp:37:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
37 | for (size_t i = 0; i < popSize; ++i) {
| ~~^~~~~~~~~
unphased.cpp: In function 'Output simulation_phased_nonphased(int, double, int, double, std::vector<double>, const Rcpp::NumericVector&, bool, bool, int, rnd_t*, size_t)':
unphased.cpp:105:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
105 | for (size_t t = 0; t <= maxTime; ++t) {
| ~~^~~~~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb.h:32,
from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel/TBB.h:10,
from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel.h:24,
from util.h:15,
from unphased.cpp:22:
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o junctions.dll tmp.def Fish.o Output.o RcppExports.o backcrossing.o estimate_time_unphased.o main_functions.o unphased.o -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64 -ltbb -ltbbmalloc -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
make[1]: Leaving directory '/d/temp/2025_06_29_01_50_00_26597/RtmpAxbSfI/R.INSTALL2d3a06582719c/junctions/src'
make[1]: Entering directory '/d/temp/2025_06_29_01_50_00_26597/RtmpAxbSfI/R.INSTALL2d3a06582719c/junctions/src'
make[1]: Leaving directory '/d/temp/2025_06_29_01_50_00_26597/RtmpAxbSfI/R.INSTALL2d3a06582719c/junctions/src'
installing to d:/Rcompile/CRANpkg/lib/4.6/00LOCK-junctions/00new/junctions/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 'junctions' as junctions_2.1.3.zip
* DONE (junctions)