Install log for 'DNAtools'

* installing *source* package ‘DNAtools’ ...
** this is package ‘DNAtools’ version ‘0.2-5’
** package ‘DNAtools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 23.1.0’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/DNAtools/src'
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c class_DNTRare.cpp -o class_DNTRare.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c compare-utils.cpp -o compare-utils.o
compare-utils.cpp:107:20: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl]
  107 |   int *pnProf1 = &(Rcpp::as<std::vector<int> >(prof1)[0]); // this should replace INTEGER(prof1)
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compare-utils.cpp:108:20: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl]
  108 |   int *pnProf2 = &(Rcpp::as<std::vector<int> >(prof2)[0]);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c compare.cpp -o compare.o
2 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c compare_threaded.cpp -o compare_threaded.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c number_of_alleles.cpp -o number_of_alleles.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c profile.cpp -o profile.o
In file included from compare_threaded.cpp:14:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/RcppParallel.h:24:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/RcppParallel/TBB.h:16:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/tbb/parallel_for.h:17:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/tbb/../oneapi/tbb/parallel_for.h:23:
/data/localhost/ripley/R/test-clang/RcppParallel/include/tbb/../oneapi/tbb/detail/_task.h:89:13: warning: unused function template 'suspend_callback' [-Wunused-template]
   89 | static void suspend_callback(void* user_callback, suspend_point sp) {
      |             ^~~~~~~~~~~~~~~~
In file included from compare_threaded.cpp:14:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/RcppParallel.h:24:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/RcppParallel/TBB.h:16:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/tbb/parallel_for.h:17:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/tbb/../oneapi/tbb/parallel_for.h:27:
In file included from /data/localhost/ripley/R/test-clang/RcppParallel/include/tbb/../oneapi/tbb/partitioner.h:47:
/data/localhost/ripley/R/test-clang/RcppParallel/include/tbb/../oneapi/tbb/task_group.h:130:15: warning: unused function template 'task_ptr_or_nullptr' [-Wunused-template]
  130 |     d1::task* task_ptr_or_nullptr(F&& f){
      |               ^~~~~~~~~~~~~~~~~~~
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppParallel/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c rare_prob.cpp -o rare_prob.o
2 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang23/lib -L/usr/local/clang23/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -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/localhost/ripley/R/packages/tests-clang/DNAtools/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/DNAtools/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/DNAtools/src'
installing to /data/localhost/ripley/R/packages/tests-clang/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)