* 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 /usr/local/clang18/bin/clang++ -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... /usr/local/clang18/bin/clang++ -std=gnu++11 -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether /usr/local/clang18/bin/clang++ -std=gnu++11 accepts -g... (cached) yes checking for gcc... /usr/local/clang18/bin/clang checking whether we are using the GNU C compiler... yes checking whether /usr/local/clang18/bin/clang accepts -g... yes checking for /usr/local/clang18/bin/clang option to accept ISO C89... none needed checking for /usr/local/clang18/bin/clang++ -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: ‘clang version 18.1.4’ using C++ compiler: ‘clang version 18.1.4’ using C++11 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/AnaCoDa/src' /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c CodonTable.cpp -o CodonTable.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c CovarianceMatrix.cpp -o CovarianceMatrix.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c FONSEModel.cpp -o FONSEModel.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c FONSEParameter.cpp -o FONSEParameter.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Gene.cpp -o Gene.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Genome.cpp -o Genome.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MCMCAlgorithm.cpp -o MCMCAlgorithm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Model.cpp -o Model.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PAModel.cpp -o PAModel.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PANSEModel.cpp -o PANSEModel.o PAModel.cpp:58:19: warning: unused variable 'currNumCodonsInMRNA' [-Wunused-variable] 58 | unsigned currNumCodonsInMRNA = gene->geneData.getCodonCountForCodon(codon); | ^~~~~~~~~~~~~~~~~~~ PANSEModel.cpp:1255:18: warning: unused variable 'lambdaCategory' [-Wunused-variable] 1255 | unsigned lambdaCategory = parameter->getSelectionCategory(mixtureElement); | ^~~~~~~~~~~~~~ /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PANSEParameter.cpp -o PANSEParameter.o 1 warning generated. 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PAParameter.cpp -o PAParameter.o PANSEParameter.cpp:844:12: warning: variable 'acceptanceUnder' set but not used [-Wunused-but-set-variable] 844 | unsigned acceptanceUnder = 0u; | ^ PANSEParameter.cpp:845:12: warning: variable 'acceptanceOver' set but not used [-Wunused-but-set-variable] 845 | unsigned acceptanceOver = 0u; | ^ /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Parameter.cpp -o Parameter.o 2 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RCPP_Model.cpp -o RCPP_Model.o Parameter.cpp:1397:9: 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:1446:12: warning: variable 'acceptanceUnder' set but not used [-Wunused-but-set-variable] 1446 | unsigned acceptanceUnder = 0u; | ^ Parameter.cpp:1447:12: warning: variable 'acceptanceOver' set but not used [-Wunused-but-set-variable] 1447 | unsigned acceptanceOver = 0u; | ^ /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RCPP_Parameter.cpp -o RCPP_Parameter.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RCPP_Trace.cpp -o RCPP_Trace.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ROCModel.cpp -o ROCModel.o 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ROCParameter.cpp -o ROCParameter.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SequenceSummary.cpp -o SequenceSummary.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Testing.cpp -o Testing.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Trace.cpp -o Trace.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c main.cpp -o main.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c registerDynamicSymbol.c -o registerDynamicSymbol.o /usr/local/clang18/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -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-clang/AnaCoDa/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/AnaCoDa/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/AnaCoDa/src' installing to /data/gannet/ripley/R/packages/tests-clang/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)