* installing *source* package ‘mums2’ ...
** this is package ‘mums2’ version ‘0.1.1’
** package ‘mums2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 23.1.0’
using C++ compiler: ‘clang version 23.1.0’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/mums2/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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 AlphaDiversity.cpp -o AlphaDiversity.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 Annotation.cpp -o Annotation.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 AnnotationController.cpp -o AnnotationController.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 BetaDiversity.cpp -o BetaDiversity.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 BrayCurtisDissimilarity.cpp -o BrayCurtisDissimilarity.o
/usr/local/clang23/bin/clang-23 -std=gnu23 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c CleanSpectrum.c -o CleanSpectrum.o
CleanSpectrum.c:139:44: warning: using static function 'printf' in an inline function with external linkage is a C2y extension [-Wstatic-in-inline]
139 | if (__DEBUG__CLEAN_SPECTRUM__) printf("mz: %f, mz_delta_allowed_left: %f, mz_delta_allowed_right: %f\n", spectrum_2d[idx][0], mz_delta_allowed_left, mz_delta_allowed_right);
| ^
./ScoringMethods/SpectralEntropy/CleanSpectrum.h:65:5: note: use 'static' to give inline function 'centroid_spectrum' internal linkage
65 | int centroid_spectrum(float_spec (*spectrum_2d)[2], int peaks_length, double min_ms2_difference_in_da, double min_ms2_difference_in_ppm, int* spectrum_argsort);
| ^
| static
/usr/include/bits/stdio2.h:135:1: note: 'printf' declared here
135 | printf (__fortify_clang_overload_arg (const char *, __restrict, __fmt), ...)
| ^
CleanSpectrum.c:148:44: warning: using static function 'printf' in an inline function with external linkage is a C2y extension [-Wstatic-in-inline]
148 | if (__DEBUG__CLEAN_SPECTRUM__) printf("idx_left: %d\n", idx_left);
| ^
./ScoringMethods/SpectralEntropy/CleanSpectrum.h:65:5: note: use 'static' to give inline function 'centroid_spectrum' internal linkage
65 | int centroid_spectrum(float_spec (*spectrum_2d)[2], int peaks_length, double min_ms2_difference_in_da, double min_ms2_difference_in_ppm, int* spectrum_argsort);
| ^
| static
/usr/include/bits/stdio2.h:135:1: note: 'printf' declared here
135 | printf (__fortify_clang_overload_arg (const char *, __restrict, __fmt), ...)
| ^
CleanSpectrum.c:155:44: warning: using static function 'printf' in an inline function with external linkage is a C2y extension [-Wstatic-in-inline]
155 | if (__DEBUG__CLEAN_SPECTRUM__) printf("idx_right: %d\n", idx_right);
| ^
./ScoringMethods/SpectralEntropy/CleanSpectrum.h:65:5: note: use 'static' to give inline function 'centroid_spectrum' internal linkage
65 | int centroid_spectrum(float_spec (*spectrum_2d)[2], int peaks_length, double min_ms2_difference_in_da, double min_ms2_difference_in_ppm, int* spectrum_argsort);
| ^
| static
/usr/include/bits/stdio2.h:135:1: note: 'printf' declared here
135 | printf (__fortify_clang_overload_arg (const char *, __restrict, __fmt), ...)
| ^
CleanSpectrum.c:161:48: warning: using static function 'printf' in an inline function with external linkage is a C2y extension [-Wstatic-in-inline]
161 | if (__DEBUG__CLEAN_SPECTRUM__) printf("i: %d, mz: %f, intensity: %f\n", i, spectrum_2d[i][0], spectrum_2d[i][1]);
| ^
./ScoringMethods/SpectralEntropy/CleanSpectrum.h:65:5: note: use 'static' to give inline function 'centroid_spectrum' internal linkage
65 | int centroid_spectrum(float_spec (*spectrum_2d)[2], int peaks_length, double min_ms2_difference_in_da, double min_ms2_difference_in_ppm, int* spectrum_argsort);
| ^
| static
/usr/include/bits/stdio2.h:135:1: note: 'printf' declared here
135 | printf (__fortify_clang_overload_arg (const char *, __restrict, __fmt), ...)
| ^
4 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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 CommunityMatrix.cpp -o CommunityMatrix.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 DecomposeMass.cpp -o DecomposeMass.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 DetectNeutralLoses.cpp -o DetectNeutralLoses.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 Distance.cpp -o Distance.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 Diversity.cpp -o Diversity.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 DiversityMetricFactory.cpp -o DiversityMetricFactory.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 FragmentationTree.cpp -o FragmentationTree.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 GreedyHeuristic.cpp -o GreedyHeuristic.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 HammingDistance.cpp -o HammingDistance.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 HumanMetabolomicsDB.cpp -o HumanMetabolomicsDB.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 JaccardDistance.cpp -o JaccardDistance.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 ModifiedCosineScore.cpp -o ModifiedCosineScore.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 MolecularFormula.cpp -o MolecularFormula.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 MolecularMakeup.cpp -o MolecularMakeup.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 MorisitahornIndex.cpp -o MorisitahornIndex.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 Rarefaction.cpp -o Rarefaction.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 ReadSpectra.cpp -o ReadSpectra.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 ScoringFactory.cpp -o ScoringFactory.o
In file included from RcppExports.cpp:5:
In file included from /data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
In file included from /data/localhost/ripley/R/test-clang/Rcpp/include/RcppCommon.h:29:
/data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp/r/check_r_headers.h:27:13: warning: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages]
27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
| ^
/data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp/r/check_r_headers.h:35:13: warning: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages]
35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
| ^
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 ShannonDiversityIndex.cpp -o ShannonDiversityIndex.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 SimpsonsDiversityIndex.cpp -o SimpsonsDiversityIndex.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 SorensonIndex.cpp -o SorensonIndex.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 SpeciesRichnessDiversity.cpp -o SpeciesRichnessDiversity.o
/usr/local/clang23/bin/clang-23 -std=gnu23 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -I'/data/localhost/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c SpectralEntropy.c -o SpectralEntropy.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 ThetaycDissimilarity.cpp -o ThetaycDissimilarity.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 alphabet.cpp -o alphabet.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 alphabettextparser.cpp -o alphabettextparser.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 annotateMs2Features.cpp -o annotateMs2Features.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 composedelement.cpp -o composedelement.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 denovo_molecular_formula_prediction.cpp -o denovo_molecular_formula_prediction.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 distMs2.cpp -o distMs2.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 distributionprobabilityscorer.cpp -o distributionprobabilityscorer.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 diversityCalculations.cpp -o diversityCalculations.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 element.cpp -o element.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 entropy.cpp -o entropy.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 humanMetabolomicsDBController.cpp -o humanMetabolomicsDBController.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 isotopedistribution.cpp -o isotopedistribution.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 moleculesequenceparser.cpp -o moleculesequenceparser.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 ms2ms1compare.cpp -o ms2ms1compare.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 progressBar.cpp -o progressBar.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 realmassdecomposer.cpp -o realmassdecomposer.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 spectrumReaders.cpp -o spectrumReaders.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 standardmoleculesequenceparser.cpp -o standardmoleculesequenceparser.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-alpha_diversity.cpp -o test-alpha_diversity.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-annotation_controller.cpp -o test-annotation_controller.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-beta_diversity.cpp -o test-beta_diversity.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-cpp_matrix.cpp -o test-cpp_matrix.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-diversity_metric_function.cpp -o test-diversity_metric_function.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-fragmentation_tree.cpp -o test-fragmentation_tree.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-greedy_heuristic.cpp -o test-greedy_heuristic.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-molecular_formula.cpp -o test-molecular_formula.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-molecular_formula_similarity.cpp -o test-molecular_formula_similarity.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-molecular_makeup.cpp -o test-molecular_makeup.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-rarefaction.cpp -o test-rarefaction.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-read_spectra.cpp -o test-read_spectra.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 test-runner.cpp -o test-runner.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/sitmo/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppThread/include' -I'/data/localhost/ripley/R/test-clang/testthat/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 weights.cpp -o weights.o
/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 mums2.so AlphaDiversity.o Annotation.o AnnotationController.o BetaDiversity.o BrayCurtisDissimilarity.o CleanSpectrum.o CommunityMatrix.o DecomposeMass.o DetectNeutralLoses.o Distance.o Diversity.o DiversityMetricFactory.o FragmentationTree.o GreedyHeuristic.o HammingDistance.o HumanMetabolomicsDB.o JaccardDistance.o ModifiedCosineScore.o MolecularFormula.o MolecularMakeup.o MorisitahornIndex.o Rarefaction.o RcppExports.o ReadSpectra.o ScoringFactory.o ShannonDiversityIndex.o SimpsonsDiversityIndex.o SorensonIndex.o SpeciesRichnessDiversity.o SpectralEntropy.o ThetaycDissimilarity.o alphabet.o alphabettextparser.o annotateMs2Features.o composedelement.o denovo_molecular_formula_prediction.o distMs2.o distributionprobabilityscorer.o diversityCalculations.o element.o entropy.o humanMetabolomicsDBController.o isotopedistribution.o moleculesequenceparser.o ms2ms1compare.o progressBar.o realmassdecomposer.o spectrumReaders.o standardmoleculesequenceparser.o test-alpha_diversity.o test-annotation_controller.o test-beta_diversity.o test-cpp_matrix.o test-diversity_metric_function.o test-fragmentation_tree.o test-greedy_heuristic.o test-molecular_formula.o test-molecular_formula_similarity.o test-molecular_makeup.o test-rarefaction.o test-read_spectra.o test-runner.o weights.o -latomic -lpthread
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/mums2/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/mums2/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/mums2/src'
installing to /data/localhost/ripley/R/packages/tests-clang/mums2.Rcheck/00LOCK-mums2/00new/mums2/libs
** R
** 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 (mums2)