* 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 clang++ -arch x86_64 -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++11 -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether clang++ -arch x86_64 -std=gnu++11 accepts -g... (cached) yes checking for gcc... clang -arch x86_64 checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking for clang++ -arch x86_64 -std=gnu++11 option to support OpenMP... unsupported 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: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CodonTable.cpp -o CodonTable.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CovarianceMatrix.cpp -o CovarianceMatrix.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FONSEModel.cpp -o FONSEModel.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FONSEParameter.cpp -o FONSEParameter.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Gene.cpp -o Gene.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Genome.cpp -o Genome.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MCMCAlgorithm.cpp -o MCMCAlgorithm.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Model.cpp -o Model.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PAModel.cpp -o PAModel.o PAModel.cpp:58:19: warning: unused variable 'currNumCodonsInMRNA' [-Wunused-variable] unsigned currNumCodonsInMRNA = gene->geneData.getCodonCountForCodon(codon); ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PANSEModel.cpp -o PANSEModel.o PANSEModel.cpp:1255:18: warning: unused variable 'lambdaCategory' [-Wunused-variable] unsigned lambdaCategory = parameter->getSelectionCategory(mixtureElement); ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PANSEParameter.cpp -o PANSEParameter.o PANSEParameter.cpp:844:12: warning: variable 'acceptanceUnder' set but not used [-Wunused-but-set-variable] unsigned acceptanceUnder = 0u; ^ PANSEParameter.cpp:845:12: warning: variable 'acceptanceOver' set but not used [-Wunused-but-set-variable] unsigned acceptanceOver = 0u; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PAParameter.cpp -o PAParameter.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Parameter.cpp -o Parameter.o Parameter.cpp:1397:9: warning: unused variable 'adjustFactor' [-Wunused-variable] double adjustFactor = 1.0; //variable assigned value of either adjustFactorLow or adjustFactorHigh depending on acceptance rate ^ Parameter.cpp:1446:12: warning: variable 'acceptanceUnder' set but not used [-Wunused-but-set-variable] unsigned acceptanceUnder = 0u; ^ Parameter.cpp:1447:12: warning: variable 'acceptanceOver' set but not used [-Wunused-but-set-variable] unsigned acceptanceOver = 0u; ^ 3 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RCPP_Model.cpp -o RCPP_Model.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RCPP_Parameter.cpp -o RCPP_Parameter.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RCPP_Trace.cpp -o RCPP_Trace.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ROCModel.cpp -o ROCModel.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ROCParameter.cpp -o ROCParameter.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SequenceSummary.cpp -o SequenceSummary.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Testing.cpp -o Testing.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Trace.cpp -o Trace.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/AnaCoDa.Rcheck/00LOCK-AnaCoDa/00new/AnaCoDa/libs ** generating debug symbols (dSYM) ** 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)