* installing *source* package ‘localScore’ ...
** this is package ‘localScore’ version ‘2.0.3’
** package ‘localScore’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
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
function_wrapper.cpp: In function ‘double daudin(int, int, Rcpp::NumericVector, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >)’:
function_wrapper.cpp:175:8: warning: unused variable ‘checkOK’ [-Wunused-variable]
  175 |   bool checkOK = checkKDMparameters(local_score, sequence_length, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
      |        ^~~~~~~
function_wrapper.cpp: In function ‘double karlin(int, int, Rcpp::NumericVector, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >)’:
function_wrapper.cpp:236:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  236 |   if(esp>=0.0)
      |   ^~
function_wrapper.cpp:239:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  239 |     double p = calcul_karlin(local_score, as<std::vector<double>>(score_probabilities), as<int>(sequence_max_), -as<int>(sequence_min_), (long)sequence_length);
      |     ^~~~~~
function_wrapper.cpp:228:8: warning: unused variable ‘checkOK’ [-Wunused-variable]
  228 |   bool checkOK = checkKDMparameters(local_score, sequence_length, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
      |        ^~~~~~~
function_wrapper.cpp: In function ‘Rcpp::NumericVector karlin_parameters(Rcpp::NumericVector, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >)’:
function_wrapper.cpp:262:8: warning: unused variable ‘checkOK’ [-Wunused-variable]
  262 |   bool checkOK = checkKDMparameters(1, 1, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
      |        ^~~~~~~
function_wrapper.cpp: In function ‘double mcc(int, int, Rcpp::NumericVector, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >)’:
function_wrapper.cpp:328:8: warning: unused variable ‘checkOK’ [-Wunused-variable]
  328 |   bool checkOK = checkKDMparameters(local_score, sequence_length, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
      |        ^~~~~~~
function_wrapper.cpp: In function ‘double maxPartialSumd(int, Rcpp::NumericVector, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >, Rcpp::Nullable<Rcpp::Vector<13> >)’:
function_wrapper.cpp:386:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  386 |   if(k<0)
      |   ^~
function_wrapper.cpp:389:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  389 |      double p = calcul_probMaxPartialSum(k, as<std::vector<double>>(score_probabilities), max_score, -min_score);
      |      ^~~~~~
function_wrapper.cpp:376:8: warning: unused variable ‘checkOK’ [-Wunused-variable]
  376 |   bool checkOK = checkKDMparameters(1, 1, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
      |        ^~~~~~~
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
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
      |       ^~~~~~~~~~~~~~~~~~~~
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
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)