* installing *source* package ‘fastglm’ ...
** package ‘fastglm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastglm/src'
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -DNDEBUG -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -DNDEBUG -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c bigmemory.cpp -o bigmemory.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -DNDEBUG -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c colmin_colmax.cpp -o colmin_colmax.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I/usr/local/include -DNDEBUG -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c fit_glm_dense.cpp -o fit_glm_dense.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from fit_glm_dense.cpp:4:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/local/gcc13/include/c++/13.2.0/memory:78,
from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10,
from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from bigmemory.cpp:4:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/local/gcc13/include/c++/13.2.0/memory:78,
from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here
65 | template<typename> class auto_ptr;
| ^~~~~~~~
bigmemory.cpp: In function 'SEXPREC* prod_vec_big(SEXP, SEXP)':
bigmemory.cpp:279:63: warning: typedef 'MatrixXchar' locally defined but not used [-Wunused-local-typedefs]
279 | typedef Eigen::Matrix<char, Eigen::Dynamic, Eigen::Dynamic> MatrixXchar;
| ^~~~~~~~~~~
bigmemory.cpp:280:64: warning: typedef 'MatrixXshort' locally defined but not used [-Wunused-local-typedefs]
280 | typedef Eigen::Matrix<short, Eigen::Dynamic, Eigen::Dynamic> MatrixXshort;
| ^~~~~~~~~~~~
bigmemory.cpp:281:50: warning: typedef 'Vectorchar' locally defined but not used [-Wunused-local-typedefs]
281 | typedef Eigen::Matrix<char, Eigen::Dynamic, 1> Vectorchar;
| ^~~~~~~~~~
bigmemory.cpp:282:51: warning: typedef 'Vectorshort' locally defined but not used [-Wunused-local-typedefs]
282 | typedef Eigen::Matrix<short, Eigen::Dynamic, 1> Vectorshort;
| ^~~~~~~~~~~
bigmemory.cpp:285:25: warning: typedef 'MapVecf' locally defined but not used [-Wunused-local-typedefs]
285 | typedef Map<VectorXf> MapVecf;
| ^~~~~~~
bigmemory.cpp: In function 'SEXPREC* prod_vec_big_right(SEXP, SEXP)':
bigmemory.cpp:349:63: warning: typedef 'MatrixXchar' locally defined but not used [-Wunused-local-typedefs]
349 | typedef Eigen::Matrix<char, Eigen::Dynamic, Eigen::Dynamic> MatrixXchar;
| ^~~~~~~~~~~
bigmemory.cpp:350:64: warning: typedef 'MatrixXshort' locally defined but not used [-Wunused-local-typedefs]
350 | typedef Eigen::Matrix<short, Eigen::Dynamic, Eigen::Dynamic> MatrixXshort;
| ^~~~~~~~~~~~
bigmemory.cpp:351:50: warning: typedef 'Vectorchar' locally defined but not used [-Wunused-local-typedefs]
351 | typedef Eigen::Matrix<char, Eigen::Dynamic, 1> Vectorchar;
| ^~~~~~~~~~
bigmemory.cpp:352:51: warning: typedef 'Vectorshort' locally defined but not used [-Wunused-local-typedefs]
352 | typedef Eigen::Matrix<short, Eigen::Dynamic, 1> Vectorshort;
| ^~~~~~~~~~~
bigmemory.cpp:355:25: warning: typedef 'MapVecf' locally defined but not used [-Wunused-local-typedefs]
355 | typedef Map<VectorXf> MapVecf;
| ^~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:341,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Dense:1,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigenForward.h:28,
from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
from ../inst/include/glm_base.h:5,
from ../inst/include/glm.h:4,
from fit_glm_dense.cpp:8:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]':
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
327 | internal::triangular_matrix_vector_product
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
332 | ::run(actualLhs.rows(),actualLhs.cols(),
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
333 | actualLhs.data(),actualLhs.outerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | actualRhsPtr,1,
| ~~~~~~~~~~~~~~~
335 | dest.data(),dest.innerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | actualAlpha);
| ~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here
105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o fastglm.so RcppExports.o bigmemory.o colmin_colmax.o fit_glm_dense.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastglm/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastglm/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastglm/src'
installing to /data/gannet/ripley/R/packages/tests-devel/fastglm.Rcheck/00LOCK-fastglm/00new/fastglm/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fastglm)