* installing *source* package 'AnaCoDa' ...
** package 'AnaCoDa' successfully unpacked and MD5 sums checked
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'g++.exe (GCC) 13.3.0'
using C++11
make[1]: Entering directory '/d/temp/2024_11_19_01_50_00_21579/RtmpWC2BUj/R.INSTALL28d38294c3a47/AnaCoDa/src'
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CodonTable.cpp -o CodonTable.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CovarianceMatrix.cpp -o CovarianceMatrix.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FONSEModel.cpp -o FONSEModel.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FONSEParameter.cpp -o FONSEParameter.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Gene.cpp -o Gene.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Genome.cpp -o Genome.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCMCAlgorithm.cpp -o MCMCAlgorithm.o
MCMCAlgorithm.cpp: In member function 'double MCMCAlgorithm::acceptRejectSynthesisRateLevelForAllGenes(Genome&, Model&, int)':
MCMCAlgorithm.cpp:112:33: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
112 | for (unsigned i = 0u; i < numGenes; i++)
| ~~^~~~~~~~~~
MCMCAlgorithm.cpp: In member function 'void MCMCAlgorithm::run(Genome&, Model&, unsigned int, unsigned int)':
MCMCAlgorithm.cpp:552:44: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
552 | for (int iteration = 1u; iteration <= maximumIterations; iteration++)
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
MCMCAlgorithm.cpp: In member function 'void MCMCAlgorithm::run_PANSE(Genome&, PANSEModel&, unsigned int, unsigned int)':
MCMCAlgorithm.cpp:701:44: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
701 | for (int iteration = 1u; iteration <= maximumIterations; iteration++)
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
MCMCAlgorithm.cpp: In static member function 'static std::vector<std::vector<double> > MCMCAlgorithm::solveToeplitzMatrix(int, std::vector<double>, std::vector<double>)':
MCMCAlgorithm.cpp:1239:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1239 | for (unsigned l = 1; l < lr; l++)
| ~~^~~~
MCMCAlgorithm.cpp:1263:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1263 | if (l == lr) return returnVec;
| ~~^~~~~
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Model.cpp -o Model.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PAModel.cpp -o PAModel.o
PAModel.cpp: In member function 'virtual void PAModel::calculateZ(std::string, Genome&, std::vector<double>&)':
PAModel.cpp:58:26: warning: unused variable 'currNumCodonsInMRNA' [-Wunused-variable]
58 | unsigned currNumCodonsInMRNA = gene->geneData.getCodonCountForCodon(codon);
| ^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PANSEModel.cpp -o PANSEModel.o
PANSEModel.cpp: In member function 'virtual void PANSEModel::simulateGenome(Genome&)':
PANSEModel.cpp:1255:18: warning: unused variable 'lambdaCategory' [-Wunused-variable]
1255 | unsigned lambdaCategory = parameter->getSelectionCategory(mixtureElement);
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PANSEParameter.cpp -o PANSEParameter.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PAParameter.cpp -o PAParameter.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Parameter.cpp -o Parameter.o
Parameter.cpp: In member function 'void Parameter::adaptSynthesisRateProposalWidth(unsigned int, bool)':
Parameter.cpp:1397:16: warning: unused variable 'adjustFactor' [-Wunused-variable]
1397 | double adjustFactor = 1.0; //variable assigned value of either adjustFactorLow or adjustFactorHigh depending on acceptance rate
| ^~~~~~~~~~~~
Parameter.cpp: In member function 'std::vector<double> Parameter::getExpressionQuantile(unsigned int, unsigned int, std::vector<double>, bool)':
Parameter.cpp:1988:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
1988 | for (int i = 0; i < probs.size();i++)
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RCPP_Model.cpp -o RCPP_Model.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RCPP_Parameter.cpp -o RCPP_Parameter.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RCPP_Trace.cpp -o RCPP_Trace.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ROCModel.cpp -o ROCModel.o
ROCModel.cpp: In member function 'virtual void ROCModel::calculateLogLikelihoodRatioPerGroupingPerCategory(std::string, Genome&, std::vector<double>&)':
ROCModel.cpp:177:33: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
177 | for (unsigned i = 0u; i < numGenes; i++)
| ~~^~~~~~~~~~
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ROCParameter.cpp -o ROCParameter.o
ROCParameter.cpp: In member function 'void ROCParameter::initROCParameterSet()':
ROCParameter.cpp:82:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
82 | for (int i=0; i < numMutationCategories; i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
ROCParameter.cpp: In member function 'void ROCParameter::initROCValuesFromFile(std::string)':
ROCParameter.cpp:324:75: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
324 | for (int i = 0; i < numMutationCategories;i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
ROCParameter.cpp:342:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
342 | for (int i = 0; i < numMutationCategories;i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SequenceSummary.cpp -o SequenceSummary.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Testing.cpp -o Testing.o
Testing.cpp: In function 'int testSequenceSummary()':
Testing.cpp:874:22: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
874 | if (iVect[i] != tmp)
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Trace.cpp -o Trace.o
g++ -std=gnu++11 -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" -fopenmp -DCPPTOML_USE_MAP -fopenmp -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.o
gcc -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 -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -shared -s -static-libgcc -o AnaCoDa.dll tmp.def CodonTable.o CovarianceMatrix.o FONSEModel.o FONSEParameter.o Gene.o Genome.o MCMCAlgorithm.o Model.o PAModel.o PANSEModel.o PANSEParameter.o PAParameter.o Parameter.o RCPP_Model.o RCPP_Parameter.o RCPP_Trace.o ROCModel.o ROCParameter.o SequenceSummary.o Testing.o Trace.o main.o registerDynamicSymbol.o -fopenmp -fopenmp -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_11_19_01_50_00_21579/RtmpWC2BUj/R.INSTALL28d38294c3a47/AnaCoDa/src'
make[1]: Entering directory '/d/temp/2024_11_19_01_50_00_21579/RtmpWC2BUj/R.INSTALL28d38294c3a47/AnaCoDa/src'
make[1]: Leaving directory '/d/temp/2024_11_19_01_50_00_21579/RtmpWC2BUj/R.INSTALL28d38294c3a47/AnaCoDa/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-AnaCoDa/00new/AnaCoDa/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 'AnaCoDa' as AnaCoDa_0.1.4.4.zip
* DONE (AnaCoDa)