* installing *source* package ‘gaston’ ...
** package ‘gaston’ 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/gaston/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 allele_recoding.cpp -o allele_recoding.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 alleles_duplicated.cpp -o alleles_duplicated.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -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 davies.c -o davies.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 duplicated_remove.cpp -o duplicated_remove.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 export-aireml-1k.cpp -o export-aireml-1k.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 export-aireml-logit-1k.cpp -o export-aireml-logit-1k.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 export-aireml-logit-nk.cpp -o export-aireml-logit-nk.o
In file included from export-aireml-logit-nk.cpp:3:
../inst/include/gaston/any.h: In function 'bool any(std::vector<bool>)':
../inst/include/gaston/any.h:4:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
4 | for(int i = 0; i < x.size(); i++)
| ~~^~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 export-aireml-nk.cpp -o export-aireml-nk.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 export-logit.cpp -o export-logit.o
In file included from ../inst/include/gaston/ai-reml-nk.h:4,
from export-aireml-nk.cpp:3:
../inst/include/gaston/any.h: In function 'bool any(std::vector<bool>)':
../inst/include/gaston/any.h:4:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
4 | for(int i = 0; i < x.size(); i++)
| ~~^~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:337,
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 ../inst/include/gaston/matrix-varia.h:3,
from export-aireml-logit-1k.cpp:2:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::Matrix<double, -1, -1>; int LhsMode = 17; Rhs = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:337,
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 ../inst/include/gaston/matrix-varia.h:3,
from export-aireml-logit-nk.cpp:2:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::Matrix<double, -1, -1>; int LhsMode = 17; Rhs = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:337,
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 ../inst/include/gaston/matrix-varia.h:3,
from export-aireml-1k.cpp:2:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::Matrix<double, -1, -1>; int LhsMode = 17; Rhs = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -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 gaston_init.c -o gaston_init.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 gwas_lm_quanti.cpp -o gwas_lm_quanti.o
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:341:
/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++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 gwas_lmm_diago_lrt.cpp -o gwas_lmm_diago_lrt.o
gwas_lm_quanti.cpp: In function 'Rcpp::List GWAS_lm_quanti(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, int, int)':
gwas_lm_quanti.cpp:35:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
35 | for(int ii = 0; ii < pA->true_ncol-1; ii++) {
| ~~~^~~~~~~~~~~~~~~~~
gwas_lm_quanti.cpp:44:41: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
44 | for(int ss = 0; ss < 4 && 4*ii+ss < pA->ncol; ss++) {
| ~~~~~~~~^~~~~~~~~~
gwas_lmm_diago_lrt.cpp: In function 'Rcpp::List GWAS_lmm_lrt(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, int, Rcpp::NumericVector, Rcpp::NumericMatrix, int, int, double)':
gwas_lmm_diago_lrt.cpp:73:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
73 | for(int ii = 0; ii < pA->true_ncol-1; ii++) {
| ~~~^~~~~~~~~~~~~~~~~
gwas_lmm_diago_lrt.cpp:82:41: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
82 | for(int ss = 0; ss < 4 && 4*ii+ss < pA->ncol; ss++) {
| ~~~~~~~~^~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:337,
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 ../inst/include/gaston/matrix-varia.h:3,
from export-aireml-nk.cpp:2:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::Matrix<double, -1, -1>; int LhsMode = 17; Rhs = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 gwas_lmm_diago_wald.cpp -o gwas_lmm_diago_wald.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 gwas_lmm_score.cpp -o gwas_lmm_score.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 gwas_logit_wald.cpp -o gwas_logit_wald.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 gwas_logitmm_wald.cpp -o gwas_logitmm_wald.o
gwas_lmm_diago_wald.cpp: In function 'Rcpp::List GWAS_lmm_wald(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, int, Rcpp::NumericVector, Rcpp::NumericMatrix, int, int, double)':
gwas_lmm_diago_wald.cpp:68:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
68 | for(int ii = 0; ii < pA->true_ncol-1; ii++) {
| ~~~^~~~~~~~~~~~~~~~~
gwas_lmm_diago_wald.cpp:77:41: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
77 | for(int ss = 0; ss < 4 && 4*ii+ss < pA->ncol; ss++) {
| ~~~~~~~~^~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 hwe.cpp -o hwe.o
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:341:
/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++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 hwe_chi.cpp -o hwe_chi.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 isnullptr.cpp -o isnullptr.o
gwas_lmm_score.cpp: In function 'Rcpp::List GWAS_lmm_score(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, int, int)':
gwas_lmm_score.cpp:21:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
21 | for(int ii = 0; ii < pA->true_ncol-1; ii++) {
| ~~~^~~~~~~~~~~~~~~~~
gwas_lmm_score.cpp:30:41: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
30 | for(int ss = 0; ss < 4 && 4*ii+ss < pA->ncol; ss++) {
| ~~~~~~~~^~~~~~~~~~
gwas_lmm_score.cpp: In function 'Rcpp::List GWAS_lmm_score_f(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, int, int)':
gwas_lmm_score.cpp:76:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
76 | for(int ii = 0; ii < pA->true_ncol-1; ii++) {
| ~~~^~~~~~~~~~~~~~~~~
gwas_lmm_score.cpp:85:41: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
85 | for(int ss = 0; ss < 4 && 4*ii+ss < pA->ncol; ss++) {
| ~~~~~~~~^~~~~~~~~~
gwas_logit_wald.cpp: In function 'Rcpp::List GWAS_logit_wald_f(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, int, int, double)':
gwas_logit_wald.cpp:37:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
37 | for(int ii = 0; ii < pA->true_ncol-1; ii++) {
| ~~~^~~~~~~~~~~~~~~~~
gwas_logit_wald.cpp:46:41: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
46 | for(int ss = 0; ss < 4 && 4*ii+ss < pA->ncol; ss++) {
| ~~~~~~~~^~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 ld_clump.cpp -o ld_clump.o
gwas_logitmm_wald.cpp: In function 'Rcpp::List GWAS_logitmm_wald_f(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, double)':
gwas_logitmm_wald.cpp:44:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
44 | for(int ii = 0; ii < pA->true_ncol-1; ii++) {
| ~~~^~~~~~~~~~~~~~~~~
gwas_logitmm_wald.cpp:53:41: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
53 | for(int ss = 0; ss < 4 && 4*ii+ss < pA->ncol; ss++) {
| ~~~~~~~~^~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 lmm_diago_fit.cpp -o lmm_diago_fit.o
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:337,
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 ../inst/include/gaston/matrix-varia.h:3,
from gwas_lmm_score.cpp:2:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::Map<Eigen::Matrix<double, -1, -1> >; int LhsMode = 17; Rhs = Eigen::Matrix<double, -1, 1>]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<float, -1, 1>; Lhs = Eigen::Matrix<float, -1, -1>; int LhsMode = 17; Rhs = Eigen::Matrix<float, -1, 1>]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const float*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = float; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 lmm_diago_full_likelihood.cpp -o lmm_diago_full_likelihood.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 lmm_diago_likelihood.cpp -o lmm_diago_likelihood.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 lmm_diago_min_max_h2.cpp -o lmm_diago_min_max_h2.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 logp_thinning.cpp -o logp_thinning.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 loubar.cpp -o loubar.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_bed.cpp -o m4_bed.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_bind_inds.cpp -o m4_bind_inds.o
m4_bed.cpp: In function 'Rcpp::XPtr<matrix4> read_bed_file(Rcpp::CharacterVector, int, int)':
m4_bed.cpp:97:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
97 | for(int j = 0; j < p_A->true_ncol; j++) {
| ~~^~~~~~~~~~~~~~~~
m4_bed.cpp: In function 'void write_bed_file(Rcpp::XPtr<matrix4>, Rcpp::CharacterVector)':
m4_bed.cpp:122:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
122 | for(int j = 0; j < p_A->true_ncol; j++) {
| ~~^~~~~~~~~~~~~~~~
m4_bind_inds.cpp: In function 'Rcpp::XPtr<matrix4> bind_inds2(Rcpp::List, Rcpp::LogicalMatrix)':
m4_bind_inds.cpp:27:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
27 | if(m != nxt->nrow) stop("Dimensions mismatch");
| ~~^~~~~~~~~~~~
m4_bind_inds.cpp:35:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
35 | for(int jj = 0; jj < nxt->ncol; jj++) {
| ~~~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:337,
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 ../inst/include/gaston/ai-reml-logit-1k-covar.h:1,
from gwas_logitmm_wald.cpp:2:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<float, -1, 1>; Lhs = Eigen::Matrix<float, -1, -1>; int LhsMode = 17; Rhs = Eigen::Matrix<float, -1, 1>]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
227 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | (
| ^
230 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
234 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | );
| ~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const float*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = float; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here
41 | void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_bind_snps.cpp -o m4_bind_snps.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_conversion.cpp -o m4_conversion.o
m4_bind_snps.cpp: In function 'Rcpp::XPtr<matrix4> bind_snps(Rcpp::List)':
m4_bind_snps.cpp:16:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
16 | if(n != nxt->ncol) Rf_error("Dimensions mismatch");
| ~~^~~~~~~~~~~~
m4_bind_snps.cpp:23:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
23 | for(int ii = 0; ii < nxt->nrow; ii++) {
| ~~~^~~~~~~~~~~
m4_conversion.cpp: In function 'Rcpp::IntegerMatrix m4_as012(Rcpp::XPtr<matrix4>)':
m4_conversion.cpp:33:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
33 | for(int i = 0; i < pA->true_ncol-1; i++) {
| ~~^~~~~~~~~~~~~~~~~
m4_conversion.cpp:42:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
42 | for(int ss = 0; ss < 4 && 4*i+ss < pA->ncol; ss++) {
| ~~~~~~~^~~~~~~~~~
m4_conversion.cpp: In function 'Rcpp::NumericMatrix m4_as_scaled_matrix_p(Rcpp::XPtr<matrix4>, Rcpp::NumericVector)':
m4_conversion.cpp:52:17: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
52 | if(p.length() != pA->nrow)
| ~~~~~~~~~~~^~~~~~~~~~~
m4_conversion.cpp:59:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
59 | for(int i = 0; i < pA->true_ncol-1; i++) {
| ~~^~~~~~~~~~~~~~~~~
m4_conversion.cpp:68:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
68 | for(int ss = 0; ss < 4 && 4*i+ss < pA->ncol; ss++) {
| ~~~~~~~^~~~~~~~~~
m4_conversion.cpp: In function 'Rcpp::NumericMatrix m4_as_scaled_matrix_mu_sigma(Rcpp::XPtr<matrix4>, Rcpp::NumericVector, Rcpp::NumericVector)':
m4_conversion.cpp:79:18: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
79 | if(mu.length() != pA->nrow || sigma.length() != pA->nrow)
| ~~~~~~~~~~~~^~~~~~~~~~~
m4_conversion.cpp:79:48: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
79 | if(mu.length() != pA->nrow || sigma.length() != pA->nrow)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~
m4_conversion.cpp:84:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
84 | for(int i = 0; i < pA->true_ncol-1; i++) {
| ~~^~~~~~~~~~~~~~~~~
m4_conversion.cpp:93:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
93 | for(int ss = 0; ss < 4 && 4*i+ss < pA->ncol; ss++) {
| ~~~~~~~^~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_dims.cpp -o m4_dims.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_exports.cpp -o m4_exports.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_extractind.cpp -o m4_extractind.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_extractsnp.cpp -o m4_extractsnp.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_kinship.cpp -o m4_kinship.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_kinship_p.cpp -o m4_kinship_p.o
m4_extractind.cpp: In function 'Rcpp::XPtr<matrix4> extract_inds_bool(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector)':
m4_extractind.cpp:11:17: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
11 | if(w.length() != pA->ncol)
| ~~~~~~~~~~~^~~~~~~~~~~
m4_extractsnp.cpp: In function 'Rcpp::XPtr<matrix4> extract_snps_bool(Rcpp::XPtr<matrix4>, Rcpp::LogicalVector)':
m4_extractsnp.cpp:13:17: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
13 | if(w.length() != pA->nrow)
| ~~~~~~~~~~~^~~~~~~~~~~
m4_extractsnp.cpp: In function 'Rcpp::XPtr<matrix4> extract_snps_indices(Rcpp::XPtr<matrix4>, Rcpp::IntegerVector)':
m4_extractsnp.cpp:32:25: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
32 | if(w(i) < 1 || w(i) > pA->nrow)
| ~~~~~^~~~~~~~~~
m4_kinship.cpp: In function 'Rcpp::NumericMatrix Kinship_w(Rcpp::XPtr<matrix4>, const std::vector<double>&, const std::vector<double>&, Rcpp::LogicalVector, int)':
m4_kinship.cpp:133:20: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
133 | if(snps.length() != p_A->nrow || mu.size() != nb_snps || w.size() != nb_snps)
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
m4_kinship.cpp:133:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
133 | if(snps.length() != p_A->nrow || mu.size() != nb_snps || w.size() != nb_snps)
| ~~~~~~~~~~^~~~~~~~~~
m4_kinship.cpp:133:69: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
133 | if(snps.length() != p_A->nrow || mu.size() != nb_snps || w.size() != nb_snps)
| ~~~~~~~~~^~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from ../inst/include/gaston/Parallel.h:2,
from m4_kinship.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = paraKin; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
m4_kinship.cpp:108:17: required from here
108 | parallelReduce(0, p_A->nrow, X, chunk);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
m4_kinship_p.cpp: In function 'Rcpp::NumericMatrix Kinship_pw(Rcpp::XPtr<matrix4>, const std::vector<double>&, Rcpp::LogicalVector, bool, int)':
m4_kinship_p.cpp:114:20: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
114 | if(snps.length() != p_A->nrow || p.size() != nb_snps)
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
m4_kinship_p.cpp:114:45: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
114 | if(snps.length() != p_A->nrow || p.size() != nb_snps)
| ~~~~~~~~~^~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from ../inst/include/gaston/Parallel.h:2,
from m4_kinship_p.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = paraKin_p; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
m4_kinship_p.cpp:123:17: required from here
123 | parallelReduce(0, nb_snps, X, chunk);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_ld.cpp -o m4_ld.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_ldp.cpp -o m4_ldp.o
m4_ld.cpp: In function 'void LD_col_0(matrix4&, bar&, bar&, int, int, int, int, lou&)':
m4_ld.cpp:138:8: warning: comparison of integer expressions of different signedness: 'const int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
138 | if(n != LD.nrow || m != LD.ncol) {
| ~~^~~~~~~~~~
m4_ld.cpp:138:24: warning: comparison of integer expressions of different signedness: 'const int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
138 | if(n != LD.nrow || m != LD.ncol) {
| ~~^~~~~~~~~~
m4_ld.cpp: In function 'void LD_col_1(matrix4&, bar&, bar&, int, int, int, int, lou&)':
m4_ld.cpp:159:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
159 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp:159:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
159 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp: In function 'void LD_col_2(matrix4&, bar&, bar&, int, int, int, int, lou&)':
m4_ld.cpp:203:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
203 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp:203:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
203 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp: In function 'void LD_col_3(matrix4&, bar&, bar&, int, int, int, int, lou&)':
m4_ld.cpp:245:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
245 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp:245:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
245 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp: In function 'void LD_col_4(matrix4&, bar&, bar&, int, int, int, int, lou&)':
m4_ld.cpp:288:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
288 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp:288:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
288 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp: In function 'void LD_chunk(matrix4&, bar&, bar&, int, int, int, int, lou&)':
m4_ld.cpp:331:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
331 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ld.cpp:331:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
331 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from ../inst/include/gaston/Parallel.h:2,
from m4_ld.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = paraLD; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
m4_ld.cpp:89:17: required from here
89 | parallelReduce(0,A.true_ncol,X,1);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
m4_ldp.cpp: In function 'void LD_col_0(matrix4&, bar&, int, int, int, int, lou&)':
m4_ldp.cpp:43:8: warning: comparison of integer expressions of different signedness: 'const int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
43 | if(n != LD.nrow || m != LD.ncol) {
| ~~^~~~~~~~~~
m4_ldp.cpp:43:24: warning: comparison of integer expressions of different signedness: 'const int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
43 | if(n != LD.nrow || m != LD.ncol) {
| ~~^~~~~~~~~~
m4_ldp.cpp: In function 'void LD_col_1(matrix4&, bar&, int, int, int, int, lou&)':
m4_ldp.cpp:64:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
64 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp:64:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
64 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp: In function 'void LD_col_2(matrix4&, bar&, int, int, int, int, lou&)':
m4_ldp.cpp:108:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
108 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp:108:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
108 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp: In function 'void LD_col_3(matrix4&, bar&, int, int, int, int, lou&)':
m4_ldp.cpp:150:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
150 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp:150:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
150 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp: In function 'void LD_col_4(matrix4&, bar&, int, int, int, int, lou&)':
m4_ldp.cpp:193:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
193 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp:193:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
193 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp: In function 'void LD_chunk(matrix4&, bar&, int, int, int, int, lou&)':
m4_ldp.cpp:236:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
236 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
m4_ldp.cpp:236:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
236 | if(c2-c1+1 != LD.nrow || d2-d1+1 != LD.ncol) {
| ~~~~~~~~^~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_ldthin_left.cpp -o m4_ldthin_left.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_ldthin_random.cpp -o m4_ldthin_random.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_ldthin_right.cpp -o m4_ldthin_right.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_prod2_ms.cpp -o m4_prod2_ms.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_prod2_p.cpp -o m4_prod2_p.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_prod_ms.cpp -o m4_prod_ms.o
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from ../inst/include/gaston/Parallel.h:2,
from m4_prod2_ms.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = paraPro2; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
m4_prod2_ms.cpp:82:17: required from here
82 | parallelReduce(0, n, X);
| ~~~~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_prod_p.cpp -o m4_prod_p.o
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from ../inst/include/gaston/Parallel.h:2,
from m4_prod_ms.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from ../inst/include/gaston/Parallel.h:2,
from m4_prod2_p.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6:
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:60:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = paraPro2_p; std::size_t = long unsigned int]'
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
m4_prod2_p.cpp:81:17: required from here
81 | parallelReduce(0, n, X);
| ~~~~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_read_vcf_2.cpp -o m4_read_vcf_2.o
In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb.h:32,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TBB.h:10,
from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:24,
from ../inst/include/gaston/Parallel.h:2,
from m4_prod_p.cpp:2:
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_recode.cpp -o m4_recode.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_stats.cpp -o m4_stats.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 m4_transpose.cpp -o m4_transpose.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 manhattan_thinning.cpp -o manhattan_thinning.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 matrix-varia.cpp -o matrix-varia.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 matrix4.cpp -o matrix4.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 pre_likelihood.cpp -o pre_likelihood.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 random_ortho.cpp -o random_ortho.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 re_likelihood.cpp -o re_likelihood.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 snp_duplicated.cpp -o snp_duplicated.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/gaston/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 snp_match.cpp -o snp_match.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o gaston.so allele_recoding.o alleles_duplicated.o davies.o duplicated_remove.o export-aireml-1k.o export-aireml-logit-1k.o export-aireml-logit-nk.o export-aireml-nk.o export-logit.o gaston_init.o gwas_lm_quanti.o gwas_lmm_diago_lrt.o gwas_lmm_diago_wald.o gwas_lmm_score.o gwas_logit_wald.o gwas_logitmm_wald.o hwe.o hwe_chi.o isnullptr.o ld_clump.o lmm_diago_fit.o lmm_diago_full_likelihood.o lmm_diago_likelihood.o lmm_diago_min_max_h2.o logp_thinning.o loubar.o m4_bed.o m4_bind_inds.o m4_bind_snps.o m4_conversion.o m4_dims.o m4_exports.o m4_extractind.o m4_extractsnp.o m4_kinship.o m4_kinship_p.o m4_ld.o m4_ldp.o m4_ldthin_left.o m4_ldthin_random.o m4_ldthin_right.o m4_prod2_ms.o m4_prod2_p.o m4_prod_ms.o m4_prod_p.o m4_read_vcf_2.o m4_recode.o m4_stats.o m4_transpose.o manhattan_thinning.o matrix-varia.o matrix4.o pre_likelihood.o random_ortho.o re_likelihood.o snp_duplicated.o snp_match.o -lz
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gaston/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/gaston/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gaston/src'
installing to /data/gannet/ripley/R/packages/tests-devel/gaston.Rcheck/00LOCK-gaston/00new/gaston/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘cbind’ in package ‘gaston’
Creating a new generic function for ‘rbind’ in package ‘gaston’
** 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 (gaston)