* installing *source* package ‘magi’ ...
** package ‘magi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/magi/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c MagiMain.cpp -o MagiMain.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c MagiSolver.cpp -o MagiSolver.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from MagiSolver.cpp:3:
./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
4 | #define NDEBUG
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppFullloglikelihood.cpp -o RcppFullloglikelihood.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppTestingUtilities.cpp -o RcppTestingUtilities.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppTranslation.cpp -o RcppTranslation.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppWrapper.cpp -o RcppWrapper.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppXthetasigma.cpp -o RcppXthetasigma.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Rcppgpsmoothing.cpp -o Rcppgpsmoothing.o
Rcppgpsmoothing.cpp:1:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
1 | #define NDEBUG
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppsolveMagi.cpp -o RcppsolveMagi.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Sampler.cpp -o Sampler.o
In file included from RcppFullloglikelihood.cpp:3:
./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
4 | #define NDEBUG
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
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
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
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
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c band.cpp -o band.o
1 warning generated.
1 warning generated.
In file included from RcppXthetasigma.cpp:3:
./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
4 | #define NDEBUG
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
1 warning generated.
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.
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c classDefinition.cpp -o classDefinition.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c dynamicalSystemModels.cpp -o dynamicalSystemModels.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c fullloglikelihood.cpp -o fullloglikelihood.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c gpcov.cpp -o gpcov.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c hmc.cpp -o hmc.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c testingUtilities.cpp -o testingUtilities.o
In file included from fullloglikelihood.cpp:3:
./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
4 | #define NDEBUG
| ^
<command line>: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
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c tgtdistr.cpp -o tgtdistr.o
tgtdistr.cpp:2:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
2 | #define NDEBUG
| ^
<command line>:2:9: note: previous definition is here
2 | #define NDEBUG 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -DNDEBUG -I'../inst/include' -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c xthetasigma.cpp -o xthetasigma.o
1 warning generated.
In file included from testingUtilities.cpp:3:
./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
4 | #define NDEBUG
| ^
<command line>: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
| ^
<command line>: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]
| ~~~^~~~~~~~~~~~~~~~~
1 warning generated.
tgtdistr.cpp:519:52: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture]
519 | fOdeModelShifted.fOdeDtheta = [&muAllDimension, &dotmuAllDimension, &fOdeModel]
| ~~~^~~~~~~~~~~~~~~~~
3 warnings generated.
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/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 -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)