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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL OncoSimulR
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
C:\rtools42\x86_64-w64-mingw32.static.posix\bin\ar.exe: creating liblandscape.a
ranlib liblandscape.a;
gcc  -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
gcc  -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c OncoSimulR_init.c -o OncoSimulR_init.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:4:
UnityOncoSimul/BNB_nr.cpp: In function 'void nr_innerBNB(const fitnessEffectsAll&, const std::vector<double>&, const double&, TypeModel, const int&, const std::vector<double>&, const double&, const double&, const double&, const std::vector<std::vector<int> >&, const time_t&, const double&, const double&, const double&, const int&, const double&, const double&, const int&, double&, double&, double&, double&, double&, int&, int&, int&, std::vector<Genotype>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<Intervention>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<int>&, bool&, std::mt19937&, double&, bool&, const std::map<int, std::__cxx11::basic_string<char> >&, const fitness_as_genes&, PhylogName&, bool, const fitnessEffectsAll&, const std::vector<int>&, const double&, const double&, const double&, const bool&, const std::vector<std::vector<int> >&, const double&, const int&, const double&, int&, int&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, POM&, Rcpp::List, Rcpp::List, Rcpp::List)':
UnityOncoSimul/BNB_nr.cpp:860:10: warning: 'minNextMutationTime' may be used uninitialized in this function [-Wmaybe-uninitialized]
  860 |   double minNextMutationTime;
      |          ^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -s -static-libgcc -o OncoSimulR.dll tmp.def OncoSimulR_init.o RcppExports.o unity_osimul.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/libs/x64
** R
** data
** 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 (OncoSimulR)