* installing *source* package ‘Racmacs’ ... ** package ‘Racmacs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Racmacs_wrappers.cpp -o Racmacs_wrappers.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Racmacs_wrappers_antigens.cpp -o Racmacs_wrappers_antigens.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Racmacs_wrappers_optimizations.cpp -o Racmacs_wrappers_optimizations.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Racmacs_wrappers_plotspec.cpp -o Racmacs_wrappers_plotspec.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Racmacs_wrappers_sera.cpp -o Racmacs_wrappers_sera.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ac_bootstrap.cpp -o ac_bootstrap.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ac_dimension_test.cpp -o ac_dimension_test.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ac_errorlines.cpp -o ac_errorlines.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' 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-O2 -c json_read_to_acmap.cpp -o json_read_to_acmap.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c json_write_from_acmap.cpp -o json_write_from_acmap.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c procrustes.cpp -o procrustes.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils_error.cpp -o utils_error.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils_euc_dist.cpp -o utils_euc_dist.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils_geometry.cpp -o utils_geometry.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils_interpolation.cpp -o utils_interpolation.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEnsmallen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rapidjsonr/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils_transformation.cpp -o utils_transformation.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Racmacs.so Racmacs_wrappers.o Racmacs_wrappers_antigens.o Racmacs_wrappers_optimizations.o Racmacs_wrappers_plotspec.o Racmacs_wrappers_sera.o RcppExports.o ac_bootstrap.o ac_dimension_test.o ac_errorlines.o ac_hemi_test.o ac_matching.o ac_merge.o ac_move_trapped_points.o ac_optim_map_stress.o ac_optimization.o ac_optimize_ag_reactivity.o ac_stress.o ac_stress_blobs.o ac_titers.o ac_utils.o acmap_map.o acmap_optimization.o acmap_point.o acmap_titers.o json_assert.o json_read_to_acmap.o json_write_from_acmap.o procrustes.o utils.o utils_error.o utils_euc_dist.o utils_geometry.o utils_interpolation.o utils_transformation.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/Racmacs.Rcheck/00LOCK-Racmacs/00new/Racmacs/libs ** generating debug symbols (dSYM) ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (Racmacs)