* installing *source* package 'mappoly' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'g++.exe (GCC) 12.3.0'
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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
hmm_elements.cpp: In function 'std::vector<std::vector<int> > index_func(int, std::vector<int>&, std::vector<int>&)':
hmm_elements.cpp:262:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  262 |       for(int j=0; (unsigned)j < p.size(); j++)
      |       ^~~
hmm_elements.cpp:264:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  264 |         for(int j=0; (unsigned)j < q.size(); j++)
      |         ^~~
hmm_elements.cpp:264:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
hmm_elements.cpp:266:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  266 |           v1[s].push_back(ip);
      |           ^~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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
hmm_single_parent.cpp: In function 'SEXPREC* est_hmm_map_single_parent(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
hmm_single_parent.cpp:215:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  215 |         for(int j=0; (unsigned)j < alpha[i][n_mrk-1].size(); j++)
      |         ^~~
hmm_single_parent.cpp:217:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  217 |           if(temp > 0)
      |           ^~
hmm_single_parent.cpp:259:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  259 |     for(int j=0; (unsigned)j < alpha[i][n_mrk-1].size(); j++)
      |     ^~~
hmm_single_parent.cpp:261:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  261 |       if(temp > 0)
      |       ^~
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mappoly_init.c -o mappoly_init.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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
pairwise_estimation_rcppparallel.cpp: In member function 'virtual void rf_two_point_parallel::operator()(std::size_t, std::size_t)':
pairwise_estimation_rcppparallel.cpp:126:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  126 |           for(rn = 1; rn < mystring.size(); rn++){
      |                       ~~~^~~~~~~~~~~~~~~~~
pairwise_estimation_rcppparallel.cpp:145:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  145 |           for(rn = 1; rn < mystring.size(); rn++){
      |                       ~~~^~~~~~~~~~~~~~~~~
pairwise_estimation_rcppparallel.cpp:157:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  157 |           for(int j=0; j < phases.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~
pairwise_estimation_rcppparallel.cpp:175:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  175 |               for(int j=0; j < z.size(); j++)
      |                            ~~^~~~~~~~~~
pairwise_estimation_rcppparallel.cpp:214:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  214 |               for(int i = 0; i < dk.size(); i++){
      |                              ~~^~~~~~~~~~~
pairwise_estimation_rcppparallel.cpp:296:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  296 |                 for(int i = 0; i < dk.size(); i++){
      |                                ~~^~~~~~~~~~~
pairwise_estimation_rcppparallel.cpp:341:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  341 |               for(int i = 0; i < dk.size(); i++){
      |                              ~~^~~~~~~~~~~
pairwise_estimation_rcppparallel.cpp:372:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  372 |                 for(int i = 0; i < dk.size(); i++){
      |                                ~~^~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include'   -I"d:/rtools43/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
read_mappoly_vcf.cpp: In function 'int get_depth(std::string, int)':
read_mappoly_vcf.cpp:173:28: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  173 |   if (vec_o_strings.size() < dp_pos) {
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
read_mappoly_vcf.cpp: In function 'std::vector<double> get_probabilities(std::string, int)':
read_mappoly_vcf.cpp:209:28: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  209 |   if (vec_o_strings.size() < pl_pos){
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
read_mappoly_vcf.cpp: In function 'Rcpp::List vcf_get_probabilities(Rcpp::StringMatrix&, int)':
read_mappoly_vcf.cpp:276:22: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  276 |       if (out.size() == size){
      |           ~~~~~~~~~~~^~~~~~~
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/4.4/RcppParallel/lib/x64 -ltbb -ltbbmalloc -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
installing to d:/RCompile/CRANincoming/R-devel/lib/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
* DONE (mappoly)