Install log for 'smer'

* installing *source* package ‘smer’ ...
** package ‘smer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c allocate_memory.cpp -o allocate_memory.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c check_openmp.cpp -o check_openmp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c computation.cpp -o computation.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_covariance_q.cpp -o compute_covariance_q.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_mom_components.cpp -o compute_mom_components.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c count_data.cpp -o count_data.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genotype.cpp -o genotype.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c hdf5_api.cpp -o hdf5_api.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c initialize_random_vectors.cpp -o initialize_random_vectors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_covariates.cpp -o read_covariates.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_genotype_mask.cpp -o read_genotype_mask.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_genotypes.cpp -o read_genotypes.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_phenotypes.cpp -o read_phenotypes.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c set_metadata.cpp -o set_metadata.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c simulate_traits.cpp -o simulate_traits.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sme.cpp -o sme.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/opt/R/arm64/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c testing_utils.cpp -o testing_utils.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o smer.so RcppExports.o allocate_memory.o check_openmp.o computation.o compute_covariance_q.o compute_mom_components.o count_data.o genotype.o hdf5_api.o initialize_random_vectors.o read_covariates.o read_genotype_mask.o read_genotypes.o read_phenotypes.o set_metadata.o simulate_traits.o sme.o test-runner.o testing_utils.o -L/usr/local/lib -L/opt/homebrew/lib -L/opt/R/arm64/lib /Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/lib/libhdf5_cpp.a /Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/lib/libhdf5.a -L/Volumes/Builds/packages/big-sur-arm64/extralib/4.4/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/homebrew/lib'
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/00LOCK-smer/00new/smer/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** 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
Error: package or namespace load failed for ‘smer’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/00LOCK-smer/00new/smer/libs/smer.so':
  dlopen(/Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/00LOCK-smer/00new/smer/libs/smer.so, 0x0006): symbol not found in flat namespace '_H5Treclaim'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/smer’