* installing *source* package ‘DNAtools’ ...
** package ‘DNAtools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/DNAtools/src'
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c class_DNTRare.cpp -o class_DNTRare.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c compare-utils.cpp -o compare-utils.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c compare.cpp -o compare.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c compare_threaded.cpp -o compare_threaded.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c number_of_alleles.cpp -o number_of_alleles.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c profile.cpp -o profile.o
compare_threaded.cpp: In constructor 'CompareWorker::CompareWorker(const std::vector<Profile*>&, size_t, int, size_t, int, bool, bool, bool, Rcpp::IntegerVector&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&)':
compare_threaded.cpp:93:22: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare]
   93 |     if (out_m.size() != (m_nNumRows * m_nNumRows)) {
      |         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include    -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   -c rare_prob.cpp -o rare_prob.o
In file included from number_of_alleles.cpp:3:
class_probsObj.h:44:16: warning: 'std::hash<Rcpp::Vector<13> >' has a base '{anonymous}::hash_container<Rcpp::Vector<13> >' which uses the anonymous namespace [-Wsubobject-linkage]
   44 |         struct hash<IntegerVector> : hash_container<IntegerVector> {};
      |                ^~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o DNAtools.so RcppExports.o class_DNTRare.o compare-utils.o compare.o compare_threaded.o number_of_alleles.o profile.o rare_prob.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/DNAtools/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/DNAtools/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/DNAtools/src'
installing to /data/gannet/ripley/R/packages/tests-devel/DNAtools.Rcheck/00LOCK-DNAtools/00new/DNAtools/libs
** R
** data
** 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 (DNAtools)