* installing *source* package 'mappoly' ...
** this is package 'mappoly' version '0.4.1'
** package 'mappoly' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'g++.exe (GCC) 14.2.0'
make[1]: Entering directory '/d/temp/2025_07_04_01_50_00_28303/Rtmp2lSNqE/R.INSTALL16ed827564653/mappoly/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calc_genoprob.cpp -o calc_genoprob.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calc_genoprob_based_on_phased_marker_blocks.cpp -o calc_genoprob_based_on_phased_marker_blocks.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calc_loglike_given_map.cpp -o calc_loglike_given_map.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c combinatorial.cpp -o combinatorial.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c est_hmm_map_based_on_phased_mrk_blocks.cpp -o est_hmm_map_based_on_phased_mrk_blocks.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c est_map_hmm_given_dose.cpp -o est_map_hmm_given_dose.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c est_map_hmm_given_prior.cpp -o est_map_hmm_given_prior.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genotypic_counts.cpp -o genotypic_counts.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_elements.cpp -o hmm_elements.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_single_parent.cpp -o hmm_single_parent.o
gcc -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c mappoly_init.c -o mappoly_init.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairwise_estimation.cpp -o pairwise_estimation.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairwise_estimation_rcppparallel.cpp -o pairwise_estimation_rcppparallel.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/tbb/tbb.h:32,
from D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/RcppParallel/TBB.h:10,
from D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/RcppParallel.h:24,
from pairwise_estimation_rcppparallel.cpp:41:
D:/RCompile/CRANpkg/lib/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_mappoly_vcf.cpp -o read_mappoly_vcf.o
g++ -std=gnu++17 -shared -s -static-libgcc -o mappoly.dll tmp.def RcppExports.o calc_genoprob.o calc_genoprob_based_on_phased_marker_blocks.o calc_loglike_given_map.o combinatorial.o est_hmm_map_based_on_phased_mrk_blocks.o est_map_hmm_given_dose.o est_map_hmm_given_prior.o genotypic_counts.o hmm_elements.o hmm_single_parent.o mappoly_init.o pairwise_estimation.o pairwise_estimation_rcppparallel.o read_mappoly_vcf.o -lz -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.1/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_07_04_01_50_00_28303/Rtmp2lSNqE/R.INSTALL16ed827564653/mappoly/src'
make[1]: Entering directory '/d/temp/2025_07_04_01_50_00_28303/Rtmp2lSNqE/R.INSTALL16ed827564653/mappoly/src'
make[1]: Leaving directory '/d/temp/2025_07_04_01_50_00_28303/Rtmp2lSNqE/R.INSTALL16ed827564653/mappoly/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-mappoly/00new/mappoly/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 'mappoly' as mappoly_0.4.1.zip
* DONE (mappoly)