* installing *source* package ‘sgd’ ...
** package ‘sgd’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/sgd/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c sgd.cpp -o sgd.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 basedef.h:7,
from sgd.cpp:1:
/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/bind/mem_fn.hpp:25,
from /data/gannet/ripley/R/test-dev/BH/include/boost/mem_fn.hpp:22,
from /data/gannet/ripley/R/test-dev/BH/include/boost/function/detail/prologue.hpp:19,
from /data/gannet/ripley/R/test-dev/BH/include/boost/function.hpp:30,
from basedef.h:8:
/data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp: At global scope:
/data/gannet/ripley/R/test-dev/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
/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 sgd.cpp:3:
model/cox_model.h: In member function 'arma::mat cox_model::gradient(unsigned int, const arma::mat&, const data_set&) const':
model/cox_model.h:26:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
26 | for (int i = j-1; i < j; --i) {
| ~~^~~
model/cox_model.h:28:13: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
28 | if (i == j-1) {
| ~~^~~~~~
model/cox_model.h:29:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
29 | for (int k = i; k < data.n_samples; ++k) {
| ~~^~~~~~~~~~~~~~~~
In file included from sgd.cpp:12:
sgd/implicit_sgd.h: In member function 'arma::mat implicit_sgd::update(unsigned int, const arma::mat&, const data_set&, cox_model&, bool&)':
sgd/implicit_sgd.h:128:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
128 | for (int i = j-1; i < j; --i) {
| ~~^~~
sgd/implicit_sgd.h:130:13: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
130 | if (i == j-1) {
| ~~^~~~~~
sgd/implicit_sgd.h:131:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
131 | for (int k = i; k < data.n_samples; ++k) {
| ~~^~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o sgd.so RcppExports.o sgd.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/sgd/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/sgd/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/sgd/src'
installing to /data/gannet/ripley/R/packages/tests-devel/sgd.Rcheck/00LOCK-sgd/00new/sgd/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (sgd)