Install log for 'smer'

* installing *source* package ‘smer’ ...
** this is package ‘smer’ version ‘0.0.1’
** package ‘smer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/smer/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c allocate_memory.cpp -o allocate_memory.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c check_openmp.cpp -o check_openmp.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c computation.cpp -o computation.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c compute_covariance_q.cpp -o compute_covariance_q.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c compute_mom_components.cpp -o compute_mom_components.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c count_data.cpp -o count_data.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c genotype.cpp -o genotype.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c hdf5_api.cpp -o hdf5_api.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c initialize_random_vectors.cpp -o initialize_random_vectors.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c read_covariates.cpp -o read_covariates.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c read_genotype_mask.cpp -o read_genotype_mask.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c read_genotypes.cpp -o read_genotypes.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c read_phenotypes.cpp -o read_phenotypes.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c set_metadata.cpp -o set_metadata.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c simulate_traits.cpp -o simulate_traits.o
simulate_traits.cpp: In function 'Rcpp::List simulate_traits_cpp(std::string, float, float, std::vector<int>, std::vector<int>, std::vector<int>)':
simulate_traits.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   80 |   for (int i = 0; i < additive_snps.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~
simulate_traits.cpp:83:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   83 |   for (int i = 0; i < gxg_group_1.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
simulate_traits.cpp:86:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   86 |   for (int i = 0; i < gxg_group_2.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c sme.cpp -o sme.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c test-runner.cpp -o test-runner.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/Rhdf5lib/include' -I'/data/gannet/ripley/R/test-dev/testthat/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  -DR_NO_REMAP -c testing_utils.cpp -o testing_utils.o
sme.cpp: In function 'Rcpp::List sme_cpp(std::string, std::string, std::string, int, int, int, std::vector<int>, int, std::string, std::string)':
sme.cpp:145:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  145 |   for (int i = 0; i < gxg_indices.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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/usr/local/gcc14/lib64 -L/usr/local/lib64 -fopenmp /data/gannet/ripley/R/test-dev/Rhdf5lib/lib/libhdf5_cpp.a /data/gannet/ripley/R/test-dev/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/smer/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/smer/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/smer/src'
installing to /data/gannet/ripley/R/packages/tests-devel/smer.Rcheck/00LOCK-smer/00new/smer/libs
** 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
** 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 (smer)