* installing *source* package ‘knnmi’ ...
** package ‘knnmi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.4’
using C++ compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/knnmi/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c CondMutualInformation.cpp -o CondMutualInformation.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MI_Matrix.cpp -o MI_Matrix.o
In file included from CondMutualInformation.cpp:22:
In file included from include/CondMutualInformation.h:23:
In file included from include/eigen3/Eigen/Core:382:
include/eigen3/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
14 | #pragma clang diagnostic pop
| ^
In file included from CondMutualInformation.cpp:22:
include/CondMutualInformation.h:49:24: warning: 'CaDrA::CondMutualInformation::compute' hides overloaded virtual function [-Woverloaded-virtual]
49 | virtual double compute(const ArrayXd &x, const ArrayXd& y, const ArrayXd& z) ;
| ^
include/MutualInformationBase.h:65:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::compute' declared here: different number of parameters (0 vs 3)
65 | virtual double compute() ;
| ^
In file included from CondMutualInformation.cpp:22:
include/CondMutualInformation.h:54:24: warning: 'CaDrA::CondMutualInformation::sum_digamma_from_neighbors' hides overloaded virtual function [-Woverloaded-virtual]
54 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec1, MapArrayConst &vec2, const vector<double> &dists) ;
| ^
include/MutualInformationBase.h:81:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::sum_digamma_from_neighbors' declared here: different number of parameters (2 vs 3)
81 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec, const vector<double> &dists) ;
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MutualInformation.cpp -o MutualInformation.o
In file included from MI_Matrix.cpp:35:
In file included from include/MutualInformation.h:24:
In file included from include/eigen3/Eigen/Core:382:
include/eigen3/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
14 | #pragma clang diagnostic pop
| ^
In file included from MI_Matrix.cpp:35:
include/MutualInformation.h:50:18: warning: 'CaDrA::MutualInformation::compute' hides overloaded virtual function [-Woverloaded-virtual]
50 | virtual double compute(const ArrayXd &x, const ArrayXd& y) ;
| ^
include/MutualInformationBase.h:65:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::compute' declared here: different number of parameters (0 vs 2)
65 | virtual double compute() ;
| ^
In file included from MI_Matrix.cpp:36:
include/MutualInformationDiscrete.h:50:18: warning: 'CaDrA::MutualInformationDiscrete::compute' hides overloaded virtual function [-Woverloaded-virtual]
50 | virtual double compute(const ArrayXd &x, const ArrayXi& y) ;
| ^
include/MutualInformationBase.h:65:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::compute' declared here: different number of parameters (0 vs 2)
65 | virtual double compute() ;
| ^
In file included from MI_Matrix.cpp:37:
include/CondMutualInformation.h:49:24: warning: 'CaDrA::CondMutualInformation::compute' hides overloaded virtual function [-Woverloaded-virtual]
49 | virtual double compute(const ArrayXd &x, const ArrayXd& y, const ArrayXd& z) ;
| ^
include/MutualInformationBase.h:65:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::compute' declared here: different number of parameters (0 vs 3)
65 | virtual double compute() ;
| ^
In file included from MI_Matrix.cpp:37:
include/CondMutualInformation.h:54:24: warning: 'CaDrA::CondMutualInformation::sum_digamma_from_neighbors' hides overloaded virtual function [-Woverloaded-virtual]
54 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec1, MapArrayConst &vec2, const vector<double> &dists) ;
| ^
include/MutualInformationBase.h:81:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::sum_digamma_from_neighbors' declared here: different number of parameters (2 vs 3)
81 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec, const vector<double> &dists) ;
| ^
3 warnings generated.
5 warnings generated.
In file included from MutualInformation.cpp:21:
In file included from include/MutualInformation.h:24:
In file included from include/eigen3/Eigen/Core:382:
include/eigen3/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
14 | #pragma clang diagnostic pop
| ^
In file included from MutualInformation.cpp:21:
include/MutualInformation.h:50:18: warning: 'CaDrA::MutualInformation::compute' hides overloaded virtual function [-Woverloaded-virtual]
50 | virtual double compute(const ArrayXd &x, const ArrayXd& y) ;
| ^
include/MutualInformationBase.h:65:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::compute' declared here: different number of parameters (0 vs 2)
65 | virtual double compute() ;
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MutualInformationBase.cpp -o MutualInformationBase.o
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MutualInformationDiscrete.cpp -o MutualInformationDiscrete.o
In file included from MutualInformationBase.cpp:22:
In file included from include/MutualInformationBase.h:24:
In file included from include/eigen3/Eigen/Core:382:
include/eigen3/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
14 | #pragma clang diagnostic pop
| ^
In file included from MutualInformationDiscrete.cpp:21:
In file included from include/MutualInformationDiscrete.h:24:
In file included from include/eigen3/Eigen/Core:382:
include/eigen3/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
14 | #pragma clang diagnostic pop
| ^
In file included from MutualInformationDiscrete.cpp:21:
include/MutualInformationDiscrete.h:50:18: warning: 'CaDrA::MutualInformationDiscrete::compute' hides overloaded virtual function [-Woverloaded-virtual]
50 | virtual double compute(const ArrayXd &x, const ArrayXi& y) ;
| ^
include/MutualInformationBase.h:65:24: note: hidden overloaded virtual function 'CaDrA::MutualInformationBase::compute' declared here: different number of parameters (0 vs 2)
65 | virtual double compute() ;
| ^
1 warning generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c knn_mi_lib.c -o knn_mi_lib.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
2 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 knnmi.so CondMutualInformation.o MI_Matrix.o MutualInformation.o MutualInformationBase.o MutualInformationDiscrete.o knn_mi_lib.o registerDynamicSymbol.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/knnmi/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/knnmi/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/knnmi/src'
installing to /data/gannet/ripley/R/packages/tests-clang/knnmi.Rcheck/00LOCK-knnmi/00new/knnmi/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (knnmi)