* installing *source* package ‘magi’ ... ** package ‘magi’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/magi/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MagiMain.cpp -o MagiMain.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MagiSolver.cpp -o MagiSolver.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppFullloglikelihood.cpp -o RcppFullloglikelihood.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppTestingUtilities.cpp -o RcppTestingUtilities.o In file included from MagiSolver.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppTranslation.cpp -o RcppTranslation.o In file included from RcppFullloglikelihood.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ 1 warning generated. In file included from RcppTestingUtilities.cpp:10: In file included from ./RcppWrapper.h:9: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppWrapper.cpp -o RcppWrapper.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppXthetasigma.cpp -o RcppXthetasigma.o 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcppgpsmoothing.cpp -o Rcppgpsmoothing.o Rcppgpsmoothing.cpp:1:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 1 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppsolveMagi.cpp -o RcppsolveMagi.o In file included from RcppWrapper.cpp:2: In file included from ./RcppWrapper.h:9: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ In file included from RcppXthetasigma.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ 1 warning generated. 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Sampler.cpp -o Sampler.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c band.cpp -o band.o 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c classDefinition.cpp -o classDefinition.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c dynamicalSystemModels.cpp -o dynamicalSystemModels.o In file included from Sampler.cpp:1: ./Sampler.h:19:10: warning: private field 'positiveSystem' is not used [-Wunused-private-field] 19 | bool positiveSystem; | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c fullloglikelihood.cpp -o fullloglikelihood.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c gpcov.cpp -o gpcov.o In file included from fullloglikelihood.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ In file included from gpcov.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c hmc.cpp -o hmc.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c testingUtilities.cpp -o testingUtilities.o 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c tgtdistr.cpp -o tgtdistr.o tgtdistr.cpp:2:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 2 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/roptim/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c xthetasigma.cpp -o xthetasigma.o In file included from testingUtilities.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ In file included from xthetasigma.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] 4 | #define NDEBUG | ^ :2:9: note: previous definition is here 2 | #define NDEBUG 1 | ^ xthetasigma.cpp:46:50: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] 46 | fOdeModelShifted.fOdeDx = [&muAllDimension, &dotmuAllDimension, &fOdeModel] | ~~~^~~~~~~~~~~~~~~~~ xthetasigma.cpp:51:54: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] 51 | fOdeModelShifted.fOdeDtheta = [&muAllDimension, &dotmuAllDimension, &fOdeModel] | ~~~^~~~~~~~~~~~~~~~~ tgtdistr.cpp:514:48: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] 514 | fOdeModelShifted.fOdeDx = [&muAllDimension, &dotmuAllDimension, &fOdeModel] | ~~~^~~~~~~~~~~~~~~~~ tgtdistr.cpp:519:52: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] 519 | fOdeModelShifted.fOdeDtheta = [&muAllDimension, &dotmuAllDimension, &fOdeModel] | ~~~^~~~~~~~~~~~~~~~~ 3 warnings generated. 1 warning generated. 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o magi.so MagiMain.o MagiSolver.o RcppExports.o RcppFullloglikelihood.o RcppTestingUtilities.o RcppTranslation.o RcppWrapper.o RcppXthetasigma.o Rcppgpsmoothing.o RcppsolveMagi.o Sampler.o band.o classDefinition.o dynamicalSystemModels.o fullloglikelihood.o gpcov.o hmc.o testingUtilities.o tgtdistr.o xthetasigma.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/magi/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/magi/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/magi/src' installing to /data/gannet/ripley/R/packages/tests-clang/magi.Rcheck/00LOCK-magi/00new/magi/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 (magi)