* installing *source* package ‘knnmi’ ...
** package ‘knnmi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/knnmi/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -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 -DR_NO_REMAP -c CondMutualInformation.cpp -o CondMutualInformation.o
In file included from include/CondMutualInformation.h:26,
from CondMutualInformation.cpp:22:
include/MutualInformationBase.h:81:24: warning: 'virtual double CaDrA::MutualInformationBase::sum_digamma_from_neighbors(CaDrA::MapArrayConst&, const std::vector<double>&)' was hidden [-Woverloaded-virtual=]
81 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec, const vector<double> &dists) ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
include/CondMutualInformation.h:54:24: note: by 'virtual double CaDrA::CondMutualInformation::sum_digamma_from_neighbors(CaDrA::MapArrayConst&, CaDrA::MapArrayConst&, const std::vector<double>&)'
54 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec1, MapArrayConst &vec2, const vector<double> &dists) ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
include/MutualInformationBase.h:65:24: warning: 'virtual double CaDrA::MutualInformationBase::compute()' was hidden [-Woverloaded-virtual=]
65 | virtual double compute() ;
| ^~~~~~~
include/CondMutualInformation.h:49:24: note: by 'virtual double CaDrA::CondMutualInformation::compute(const Eigen::ArrayXd&, const Eigen::ArrayXd&, const Eigen::ArrayXd&)'
49 | virtual double compute(const ArrayXd &x, const ArrayXd& y, const ArrayXd& z) ;
| ^~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -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 -DR_NO_REMAP -c MI_Matrix.cpp -o MI_Matrix.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -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 -DR_NO_REMAP -c MutualInformation.cpp -o MutualInformation.o
In file included from include/MutualInformation.h:27,
from MI_Matrix.cpp:35:
include/MutualInformationBase.h:65:24: warning: 'virtual double CaDrA::MutualInformationBase::compute()' was hidden [-Woverloaded-virtual=]
65 | virtual double compute() ;
| ^~~~~~~
include/MutualInformation.h:50:18: note: by 'virtual double CaDrA::MutualInformation::compute(const Eigen::ArrayXd&, const Eigen::ArrayXd&)'
50 | virtual double compute(const ArrayXd &x, const ArrayXd& y) ;
| ^~~~~~~
include/MutualInformationBase.h:65:24: warning: 'virtual double CaDrA::MutualInformationBase::compute()' was hidden [-Woverloaded-virtual=]
65 | virtual double compute() ;
| ^~~~~~~
In file included from MI_Matrix.cpp:36:
include/MutualInformationDiscrete.h:50:18: note: by 'virtual double CaDrA::MutualInformationDiscrete::compute(const Eigen::ArrayXd&, const Eigen::ArrayXi&)'
50 | virtual double compute(const ArrayXd &x, const ArrayXi& y) ;
| ^~~~~~~
include/MutualInformationBase.h:81:24: warning: 'virtual double CaDrA::MutualInformationBase::sum_digamma_from_neighbors(CaDrA::MapArrayConst&, const std::vector<double>&)' was hidden [-Woverloaded-virtual=]
81 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec, const vector<double> &dists) ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from MI_Matrix.cpp:37:
include/CondMutualInformation.h:54:24: note: by 'virtual double CaDrA::CondMutualInformation::sum_digamma_from_neighbors(CaDrA::MapArrayConst&, CaDrA::MapArrayConst&, const std::vector<double>&)'
54 | virtual double sum_digamma_from_neighbors(MapArrayConst &vec1, MapArrayConst &vec2, const vector<double> &dists) ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
include/MutualInformationBase.h:65:24: warning: 'virtual double CaDrA::MutualInformationBase::compute()' was hidden [-Woverloaded-virtual=]
65 | virtual double compute() ;
| ^~~~~~~
include/CondMutualInformation.h:49:24: note: by 'virtual double CaDrA::CondMutualInformation::compute(const Eigen::ArrayXd&, const Eigen::ArrayXd&, const Eigen::ArrayXd&)'
49 | virtual double compute(const ArrayXd &x, const ArrayXd& y, const ArrayXd& z) ;
| ^~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -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 -DR_NO_REMAP -c MutualInformationBase.cpp -o MutualInformationBase.o
In file included from include/MutualInformation.h:27,
from MutualInformation.cpp:21:
include/MutualInformationBase.h:65:24: warning: 'virtual double CaDrA::MutualInformationBase::compute()' was hidden [-Woverloaded-virtual=]
65 | virtual double compute() ;
| ^~~~~~~
include/MutualInformation.h:50:18: note: by 'virtual double CaDrA::MutualInformation::compute(const Eigen::ArrayXd&, const Eigen::ArrayXd&)'
50 | virtual double compute(const ArrayXd &x, const ArrayXd& y) ;
| ^~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -Iinclude/ -Iinclude/eigen3/ -DNDEBUG -DEIGEN_NO_DEBUG -DEIGEN_NO_IO -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 -DR_NO_REMAP -c MutualInformationDiscrete.cpp -o MutualInformationDiscrete.o
In file included from include/MutualInformationDiscrete.h:27,
from MutualInformationDiscrete.cpp:21:
include/MutualInformationBase.h:65:24: warning: 'virtual double CaDrA::MutualInformationBase::compute()' was hidden [-Woverloaded-virtual=]
65 | virtual double compute() ;
| ^~~~~~~
include/MutualInformationDiscrete.h:50:18: note: by 'virtual double CaDrA::MutualInformationDiscrete::compute(const Eigen::ArrayXd&, const Eigen::ArrayXi&)'
50 | virtual double compute(const ArrayXd &x, const ArrayXi& y) ;
| ^~~~~~~
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 knn_mi_lib.c -o knn_mi_lib.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 registerDynamicSymbol.c -o registerDynamicSymbol.o
knn_mi_lib.c: In function '_cond_mutual_inf':
knn_mi_lib.c:290:9: warning: 'mi' may be used uninitialized [-Wmaybe-uninitialized]
290 | return( mi );
| ^
knn_mi_lib.c:192:8: note: 'mi' was declared here
192 | SEXP mi ;
| ^~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/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-devel/knnmi/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/knnmi/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/knnmi/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)