* installing *source* package ‘localScore’ ...
** this is package ‘localScore’ version ‘2.0.1’
** package ‘localScore’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/localScore/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 function_wrapper.cpp -o function_wrapper.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 localScoreC.cpp -o localScoreC.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 pValueMethods.cpp -o pValueMethods.o
localScoreC.cpp: In instantiation of ‘Rcpp::List localScoreC_T(const Rcpp::Vector<RTYPE, Rcpp::PreserveStorage>&, bool) [with int RTYPE = 13; Rcpp::List = Rcpp::Vector<19>]’:
localScoreC.cpp:176:25: required from here
176 | return localScoreC_T(as<IntegerVector>(v),suppressWarnings) ;
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
localScoreC.cpp:93:7: warning: unused variable ‘fixNoScoreMatrixSize’ [-Wunused-variable]
93 | int fixNoScoreMatrixSize = (numberOfLocalScores==0) ? 1 : 0; // needed to create finalScores Matrix in case of no localScore found
| ^~~~~~~~~~~~~~~~~~~~
localScoreC.cpp: In instantiation of ‘Rcpp::List localScoreC_T(const Rcpp::Vector<RTYPE, Rcpp::PreserveStorage>&, bool) [with int RTYPE = 14; Rcpp::List = Rcpp::Vector<19>]’:
localScoreC.cpp:179:25: required from here
179 | return localScoreC_T(as<NumericVector>(v),suppressWarnings) ;
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
localScoreC.cpp:93:7: warning: unused variable ‘fixNoScoreMatrixSize’ [-Wunused-variable]
93 | int fixNoScoreMatrixSize = (numberOfLocalScores==0) ? 1 : 0; // needed to create finalScores Matrix in case of no localScore found
| ^~~~~~~~~~~~~~~~~~~~
pValueMethods.cpp: In function ‘std::vector<double> calcul_deltaI_Complexe(RootTypes, std::vector<double>, int, int)’:
pValueMethods.cpp:369:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
369 | for (t = 0; t<cSize; t++){ // initialisation de la ligne avec des 0
| ~^~~~~~
pValueMethods.cpp:380:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
380 | for(s = 0; s<lSize; s++)
| ~^~~~~~
pValueMethods.cpp: In function ‘double calcul_probMaxPartialSum(int, std::vector<double>, int, int)’:
pValueMethods.cpp:426:45: warning: comparison of integer expressions of different signedness: ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
426 | if(roots_separated.mod_smaller_one.size() != u){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
pValueMethods.cpp:430:50: warning: comparison of integer expressions of different signedness: ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
430 | if(roots_separated.mod_greaterequal_one.size() != v){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
pValueMethods.cpp: In function ‘std::vector<double> calcul_karlin_parameters(std::vector<double>, int, int)’:
pValueMethods.cpp:533:45: warning: comparison of integer expressions of different signedness: ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
533 | if(roots_separated.mod_smaller_one.size() != u){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
pValueMethods.cpp:537:50: warning: comparison of integer expressions of different signedness: ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
537 | if(roots_separated.mod_greaterequal_one.size() != v){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
pValueMethods.cpp:512:16: warning: unused variable ‘i’ [-Wunused-variable]
512 | unsigned int i ;
| ^
pValueMethods.cpp: In function ‘double calcul_karlin(int, std::vector<double>, int, int, long int)’:
pValueMethods.cpp:609:27: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
609 | if (distribution.size() != (u+v+1)) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
pValueMethods.cpp:629:10: warning: unused variable ‘K_plus’ [-Wunused-variable]
629 | double K_plus = karlin_parameters[1] ;
| ^~~~~~
pValueMethods.cpp: In function ‘double calcul_mcc(int, std::vector<double>, int, int, long int)’:
pValueMethods.cpp:679:45: warning: comparison of integer expressions of different signedness: ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
679 | if(roots_separated.mod_smaller_one.size() != u){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
pValueMethods.cpp:683:50: warning: comparison of integer expressions of different signedness: ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
683 | if(roots_separated.mod_greaterequal_one.size() != v){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
pValueMethods.cpp:713:10: warning: unused variable ‘R’ [-Wunused-variable]
713 | double R = roots_separated.mod_smaller_one[0].real();
| ^
In file included from Eigen/Core:341,
from Eigen/Dense:1,
from pValueMethods.h:5,
from pValueMethods.cpp:10:
Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
327 | internal::triangular_matrix_vector_product
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
332 | ::run(actualLhs.rows(),actualLhs.cols(),
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
333 | actualLhs.data(),actualLhs.outerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | actualRhsPtr,1,
| ~~~~~~~~~~~~~~~
335 | dest.data(),dest.innerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | actualAlpha);
| ~~~~~~~~~~~~
Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o localScore.so RcppExports.o function_wrapper.o localScoreC.o pValueMethods.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/localScore/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/localScore/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/localScore/src'
installing to /data/gannet/ripley/R/packages/tests-devel/localScore.Rcheck/00LOCK-localScore/00new/localScore/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (localScore)