* 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: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/mums2/src' g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 AlphaDiversity.cpp -o AlphaDiversity.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 Annotation.cpp -o Annotation.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 AnnotationController.cpp -o AnnotationController.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 BetaDiversity.cpp -o BetaDiversity.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 BrayCurtisDissimilarity.cpp -o BrayCurtisDissimilarity.o gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c CleanSpectrum.c -o CleanSpectrum.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 CommunityMatrix.cpp -o CommunityMatrix.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 DecomposeMass.cpp -o DecomposeMass.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 DetectNeutralLoses.cpp -o DetectNeutralLoses.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 Distance.cpp -o Distance.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 Diversity.cpp -o Diversity.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 DiversityMetricFactory.cpp -o DiversityMetricFactory.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 FragmentationTree.cpp -o FragmentationTree.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 GreedyHeuristic.cpp -o GreedyHeuristic.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 HammingDistance.cpp -o HammingDistance.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 HumanMetabolomicsDB.cpp -o HumanMetabolomicsDB.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 JaccardDistance.cpp -o JaccardDistance.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 ModifiedCosineScore.cpp -o ModifiedCosineScore.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 MolecularFormula.cpp -o MolecularFormula.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 MolecularMakeup.cpp -o MolecularMakeup.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 MorisitahornIndex.cpp -o MorisitahornIndex.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 Rarefaction.cpp -o Rarefaction.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 In file included from /data/localhost/ripley/R/test-dev/Rcpp/include/RcppCommon.h:29, from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from RcppExports.cpp:5: /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#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’ 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-dev/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: ‘#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’ 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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 ReadSpectra.cpp -o ReadSpectra.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 ScoringFactory.cpp -o ScoringFactory.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 ShannonDiversityIndex.cpp -o ShannonDiversityIndex.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 SimpsonsDiversityIndex.cpp -o SimpsonsDiversityIndex.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 SorensonIndex.cpp -o SorensonIndex.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 SpeciesRichnessDiversity.cpp -o SpeciesRichnessDiversity.o gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SpectralEntropy.c -o SpectralEntropy.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 ThetaycDissimilarity.cpp -o ThetaycDissimilarity.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 alphabet.cpp -o alphabet.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 alphabettextparser.cpp -o alphabettextparser.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 annotateMs2Features.cpp -o annotateMs2Features.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 composedelement.cpp -o composedelement.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 denovo_molecular_formula_prediction.cpp -o denovo_molecular_formula_prediction.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 distMs2.cpp -o distMs2.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 distributionprobabilityscorer.cpp -o distributionprobabilityscorer.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 diversityCalculations.cpp -o diversityCalculations.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 element.cpp -o element.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 entropy.cpp -o entropy.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 humanMetabolomicsDBController.cpp -o humanMetabolomicsDBController.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 isotopedistribution.cpp -o isotopedistribution.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 moleculesequenceparser.cpp -o moleculesequenceparser.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 ms2ms1compare.cpp -o ms2ms1compare.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 progressBar.cpp -o progressBar.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 realmassdecomposer.cpp -o realmassdecomposer.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 spectrumReaders.cpp -o spectrumReaders.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 standardmoleculesequenceparser.cpp -o standardmoleculesequenceparser.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-alpha_diversity.cpp -o test-alpha_diversity.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-annotation_controller.cpp -o test-annotation_controller.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-beta_diversity.cpp -o test-beta_diversity.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-cpp_matrix.cpp -o test-cpp_matrix.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-diversity_metric_function.cpp -o test-diversity_metric_function.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-fragmentation_tree.cpp -o test-fragmentation_tree.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-greedy_heuristic.cpp -o test-greedy_heuristic.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-molecular_formula.cpp -o test-molecular_formula.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-molecular_formula_similarity.cpp -o test-molecular_formula_similarity.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-molecular_makeup.cpp -o test-molecular_makeup.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-rarefaction.cpp -o test-rarefaction.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-read_spectra.cpp -o test-read_spectra.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 test-runner.cpp -o test-runner.o g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/sitmo/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/testthat/include' -I'/data/localhost/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 weights.cpp -o weights.o g++ -std=gnu++20 -shared -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-devel/mums2/src' make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/mums2/src' make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/mums2/src' installing to /data/localhost/ripley/R/packages/tests-devel/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)