* installing *source* package ‘AnaCoDa’ ... ** package ‘AnaCoDa’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++-13 -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... g++-13 -std=gnu++11 -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++-13 -std=gnu++11 accepts -g... (cached) yes checking for gcc... gcc-13 checking whether we are using the GNU C compiler... yes checking whether gcc-13 accepts -g... yes checking for gcc-13 option to accept ISO C89... none needed checking for g++-13 -std=gnu++11 option to support OpenMP... -fopenmp checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for size_t... yes checking for sqrt... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using C++ compiler: ‘g++-13 (GCC) 13.2.0’ using C++11 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/AnaCoDa/src' g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c CodonTable.cpp -o CodonTable.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c CovarianceMatrix.cpp -o CovarianceMatrix.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c FONSEModel.cpp -o FONSEModel.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c FONSEParameter.cpp -o FONSEParameter.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Gene.cpp -o Gene.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Genome.cpp -o Genome.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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++) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Model.cpp -o Model.o 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 > MCMCAlgorithm::solveToeplitzMatrix(int, std::vector, std::vector)': 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++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c PAModel.cpp -o PAModel.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c PANSEModel.cpp -o PANSEModel.o PAModel.cpp: In member function 'virtual void PAModel::calculateZ(std::string, Genome&, std::vector&)': PAModel.cpp:58:26: warning: unused variable 'currNumCodonsInMRNA' [-Wunused-variable] 58 | unsigned currNumCodonsInMRNA = gene->geneData.getCodonCountForCodon(codon); | ^~~~~~~~~~~~~~~~~~~ g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c PANSEParameter.cpp -o PANSEParameter.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c PAParameter.cpp -o PAParameter.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Parameter.cpp -o Parameter.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); | ^~~~~~~~~~~~~~ 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 Parameter::getExpressionQuantile(unsigned int, unsigned int, std::vector, bool)': Parameter.cpp:1988:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1988 | for (int i = 0; i < probs.size();i++) | ~~^~~~~~~~~~~~~~ g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RCPP_Model.cpp -o RCPP_Model.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RCPP_Parameter.cpp -o RCPP_Parameter.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RCPP_Trace.cpp -o RCPP_Trace.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ROCModel.cpp -o ROCModel.o ROCModel.cpp: In member function 'virtual void ROCModel::calculateLogLikelihoodRatioPerGroupingPerCategory(std::string, Genome&, std::vector&)': 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++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ROCParameter.cpp -o ROCParameter.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SequenceSummary.cpp -o SequenceSummary.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Testing.cpp -o Testing.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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ Testing.cpp: In function 'int testSequenceSummary()': Testing.cpp:874:22: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits, unsigned int>::value_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 874 | if (iVect[i] != tmp) g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Trace.cpp -o Trace.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c main.cpp -o main.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o AnaCoDa.so 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 make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/AnaCoDa/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/AnaCoDa/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/AnaCoDa/src' installing to /data/gannet/ripley/R/packages/tests-devel/AnaCoDa.Rcheck/00LOCK-AnaCoDa/00new/AnaCoDa/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnaCoDa)