* installing *source* package ‘GAGAs’ ...
** package ‘GAGAs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GAGAs/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 LM_GAGA.cpp -o LM_GAGA.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 cox_GAGA.cpp -o cox_GAGA.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 helper_function.cpp -o helper_function.o
LM_GAGA.cpp: In function 'Eigen::MatrixXd cpp_omp(const Eigen::MatrixXd&, const Eigen::MatrixXd&, int, double)':
LM_GAGA.cpp:22:10: warning: variable 'tmp1' set but not used [-Wunused-but-set-variable]
22 | double tmp1;
| ^~~~
LM_GAGA.cpp: In function 'Rcpp::List rcpp_lm_gaga(Eigen::MatrixXd, Eigen::MatrixXd, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
LM_GAGA.cpp:220:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
220 | for (int k = 0; k < idx1.size(); k++) {
| ~~^~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 logistic_GAGA.cpp -o logistic_GAGA.o
LM_GAGA.cpp:374:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
374 | for (int k = 0; k < idx.size(); k++) {
| ~~^~~~~~~~~~~~
LM_GAGA.cpp:384:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
384 | for (int k = 0; k < idx1.size(); k++) {
| ~~^~~~~~~~~~~~~
LM_GAGA.cpp:310:9: warning: unused variable 'N_R' [-Wunused-variable]
310 | int N_R = R.rows();
| ^~~
LM_GAGA.cpp:311:9: warning: unused variable 'P_R' [-Wunused-variable]
311 | int P_R = R.cols();
| ^~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 multinomial_GAGA.cpp -o multinomial_GAGA.o
helper_function.cpp: In function 'double myfmin(double, double, double (*)(double, const std::vector<const Eigen::Matrix<double, -1, -1>*>&), int, double, const std::vector<const Eigen::Matrix<double, -1, -1>*>&)':
helper_function.cpp:52:3: warning: label 'goto30' defined but not used [-Wunused-label]
52 | goto30:
| ^~~~~~
helper_function.cpp:70:9: warning: 'e' may be used uninitialized [-Wmaybe-uninitialized]
70 | d = c*e;
| ~~^~~~~
helper_function.cpp:3:22: note: 'e' was declared here
3 | double a, b, c, d, e, eps, xm, p, q, r, tol1, tol2, u, v, w;
| ^
helper_function.cpp:76:15: warning: 'u' may be used uninitialized [-Wmaybe-uninitialized]
76 | fu = f(u, Plist);
| ~^~~~~~~~~~
helper_function.cpp:3:55: note: 'u' was declared here
3 | double a, b, c, d, e, eps, xm, p, q, r, tol1, tol2, u, v, w;
| ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/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 poisson_GAGA.cpp -o poisson_GAGA.o
cox_GAGA.cpp: In function 'Eigen::MatrixXd getEb_COX(const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, Eigen::MatrixXd&, int, bool)':
cox_GAGA.cpp:319:7: warning: unused variable 'n' [-Wunused-variable]
319 | int n = X.rows();
| ^
cox_GAGA.cpp:324:10: warning: variable 'v' set but not used [-Wunused-but-set-variable]
324 | double v;
| ^
cox_GAGA.cpp: In function 'Rcpp::List cpp_COX_gaga(Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, double, int, double, bool, double, bool, int)':
cox_GAGA.cpp:375:10: warning: unused variable 'eps' [-Wunused-variable]
375 | double eps = 1.e-19;
| ^~~
logistic_GAGA.cpp: In function 'Eigen::MatrixXd getEb_logistic(const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, Eigen::MatrixXd&, int, bool)':
logistic_GAGA.cpp:86:7: warning: unused variable 'n' [-Wunused-variable]
86 | int n = X.rows();
| ^
logistic_GAGA.cpp: In function 'Rcpp::List cpp_logistic_gaga(Eigen::MatrixXd, Eigen::MatrixXd, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
logistic_GAGA.cpp:153:10: warning: unused variable 'eps' [-Wunused-variable]
153 | double eps = 1.e-19;
| ^~~
logistic_GAGA.cpp:154:7: warning: unused variable 'n' [-Wunused-variable]
154 | int n = X.rows();
| ^
multinomial_GAGA.cpp: In function 'double Func_u_multinomial(const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&)':
multinomial_GAGA.cpp:13:10: warning: unused variable 'eps' [-Wunused-variable]
13 | double eps = 2.2204e-16;
| ^~~
multinomial_GAGA.cpp: In function 'Eigen::MatrixXd getEb_multinomial(const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, Eigen::MatrixXd&, int, bool)':
multinomial_GAGA.cpp:96:7: warning: unused variable 'N' [-Wunused-variable]
96 | int N = X.rows();
| ^
multinomial_GAGA.cpp: In function 'Rcpp::List cpp_multinomial_gaga(Eigen::MatrixXd, Eigen::MatrixXd, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
multinomial_GAGA.cpp:164:10: warning: unused variable 'eps' [-Wunused-variable]
164 | double eps = 1.e-19;
| ^~~
multinomial_GAGA.cpp:165:7: warning: unused variable 'N' [-Wunused-variable]
165 | int N = X.rows();
| ^
poisson_GAGA.cpp: In function 'Eigen::MatrixXd getEb_poisson(const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, Eigen::MatrixXd&, int, bool)':
poisson_GAGA.cpp:61:7: warning: unused variable 'n' [-Wunused-variable]
61 | int n = X.rows();
| ^
poisson_GAGA.cpp: In function 'Rcpp::List cpp_poisson_gaga(Eigen::MatrixXd, Eigen::MatrixXd, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
poisson_GAGA.cpp:127:10: warning: unused variable 'eps' [-Wunused-variable]
127 | double eps = 1.e-19;
| ^~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:341,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Dense:1,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigenForward.h:28,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
from LM_GAGA.cpp:3:
/data/gannet/ripley/R/test-dev/RcppEigen/include/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]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/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);
| ~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppEigen/include/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++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o GAGAs.so LM_GAGA.o RcppExports.o cox_GAGA.o helper_function.o logistic_GAGA.o multinomial_GAGA.o poisson_GAGA.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GAGAs/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GAGAs/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GAGAs/src'
installing to /data/gannet/ripley/R/packages/tests-devel/GAGAs.Rcheck/00LOCK-GAGAs/00new/GAGAs/libs
** R
** 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 (GAGAs)