* installing *source* package ‘MinTriadic’ ...
** this is package ‘MinTriadic’ version ‘1.0.0’
** package ‘MinTriadic’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/MinTriadic/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/lolog/include' -I'/data/gannet/ripley/R/test-dev/BH/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 MinTriadicClosure.cpp -o MinTriadicClosure.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
from /data/gannet/ripley/R/test-dev/lolog/include/Vertex.h:8,
from /data/gannet/ripley/R/test-dev/lolog/include/DirectedVertex.h:6,
from /data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:12,
from /data/gannet/ripley/R/test-dev/lolog/include/lolog.h:6,
from MinTriadicClosure.h:5,
from MinTriadicClosure.cpp:2:
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
294 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/15/memory:80,
from /data/gannet/ripley/R/test-dev/lolog/include/Vertex.h:7:
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
354 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
365 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
423 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
430 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
59 | 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:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
432 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
/usr/include/c++/15/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::refreshIds()’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1073:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1073 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In constructor ‘lolog::Directed::Directed(const lolog::Directed&, bool)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1109:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1109 | for(int i=0;i<net.verts.size();i++){
| ~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::reorderVertices(std::vector<int>)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1175:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1175 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::emptyGraph()’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1199:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1199 | for(int i=0;i < verts.size();i++){
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::setAllDyadsMissing(std::vector<int>, bool)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1245:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1245 | for(int i=0;i<nodes.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1249:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1249 | for(int i=0;i<nodes.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::pair<int, int> lolog::Directed::randomEdge() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1372:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1372 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘boost::shared_ptr<std::vector<std::pair<int, int> > > lolog::Directed::edgelist() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1435:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1435 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘Rcpp::IntegerMatrix lolog::Directed::edgelistR(bool) const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1450:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<int, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1450 | for(int i=0;i<v->size();i++){
| ~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1458:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<int, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1458 | for(int i=0;i<v->size();i++){
| ~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<std::__cxx11::basic_string<char> > lolog::Directed::continVarNames() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1470:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<lolog::ContinAttrib>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1470 | for(int i=0;i<contMeta->size();i++)
| ~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::removeContinVariable(int)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1508:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1508 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::addContinVariable(const std::vector<double>&, lolog::ContinAttrib&)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1515:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1515 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<std::__cxx11::basic_string<char> > lolog::Directed::discreteVarNames() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1522:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<lolog::DiscreteAttrib>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1522 | for(int i=0;i<disMeta->size();i++)
| ~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::removeDiscreteVariable(int)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1533:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1533 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<int> lolog::Directed::discreteVariableValues(int) const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1540:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1540 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<std::__cxx11::basic_string<char> > lolog::Directed::discreteVariable(int) const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1559:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1559 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::addDiscreteVariable(const std::vector<int>&, lolog::DiscreteAttrib&)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1567:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::DirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1567 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::addDiscreteVariableR(SEXP, std::string)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1607:24: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1607 | if(vals.size() != this->size())
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1621:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1621 | for(int i=0;i<missing.size();i++){
| ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘Rcpp::RObject lolog::Directed::getVariableR(std::string, bool)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1629:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1629 | for(int i=0;i<names.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1649:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1649 | for(int i=0;i<names.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Directed::setVariableR(SEXP, std::string)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1712:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1712 | for(int i=0;i<missing.size();i++){
| ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::refreshIds()’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1750:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1750 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In constructor ‘lolog::Undirected::Undirected(const lolog::Undirected&, bool)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1789:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1789 | for(int i=0;i<net.verts.size();i++){
| ~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::reorderVertices(std::vector<int>)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1854:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1854 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::emptyGraph()’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1877:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1877 | for(int i=0;i < verts.size();i++){
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::setAllDyadsMissing(std::vector<int>, bool)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1932:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1932 | for(int i=0;i<nodes.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1939:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1939 | for(int i=0;i<nodes.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::pair<int, int> lolog::Undirected::randomEdge() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2067:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2067 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘boost::shared_ptr<std::vector<std::pair<int, int> > > lolog::Undirected::edgelist() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2127:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2127 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘Rcpp::IntegerMatrix lolog::Undirected::edgelistR(bool) const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<int, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2144 | for(int i=0;i<v->size();i++){
| ~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2152:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<int, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2152 | for(int i=0;i<v->size();i++){
| ~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<std::__cxx11::basic_string<char> > lolog::Undirected::continVarNames() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2164:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<lolog::ContinAttrib>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2164 | for(int i=0;i<contMeta->size();i++)
| ~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::removeContinVariable(int)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2203:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2203 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::addContinVariable(const std::vector<double>&, lolog::ContinAttrib&)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2210 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<std::__cxx11::basic_string<char> > lolog::Undirected::discreteVarNames() const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2217:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<lolog::DiscreteAttrib>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2217 | for(int i=0;i<disMeta->size();i++)
| ~^~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::removeDiscreteVariable(int)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2228:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2228 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<int> lolog::Undirected::discreteVariableValues(int) const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2235:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2235 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘std::vector<std::__cxx11::basic_string<char> > lolog::Undirected::discreteVariable(int) const’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2254:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2254 | for(int i=0;i<verts.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::addDiscreteVariable(const std::vector<int>&, lolog::DiscreteAttrib&)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2262:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<boost::shared_ptr<lolog::UndirectedVertex> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2262 | for(int i=0;i<verts.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::addDiscreteVariableR(Rcpp::RObject, std::string)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2300:24: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
2300 | if(vals.size() != this->size())
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2315:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2315 | for(int i=0;i<missing.size();i++){
| ~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘Rcpp::RObject lolog::Undirected::getVariableR(std::string, bool)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2323:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2323 | for(int i=0;i<names.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2343:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2343 | for(int i=0;i<names.size();i++)
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h: In member function ‘void lolog::Undirected::setVariableR(SEXP, std::string)’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:2410:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2410 | for(int i=0;i<missing.size();i++){
| ~^~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:15:
/data/gannet/ripley/R/test-dev/lolog/include/util.h: In instantiation of ‘int lolog::indexOf(const T&, const std::vector<T>&) [with T = std::__cxx11::basic_string<char>]’:
/data/gannet/ripley/R/test-dev/lolog/include/BinaryNet.h:1620:28: required from here
1620 | int index = indexOf(name,discreteVarNames());
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/util.h:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
79 | for(int i=0;i<vec.size();i++){
| ~^~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/lolog/include/Model.h:4,
from /data/gannet/ripley/R/test-dev/lolog/include/LatentOrderLikelihood.h:4,
from /data/gannet/ripley/R/test-dev/lolog/include/lolog.h:9:
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h: In instantiation of ‘std::vector<double> lolog::BaseStat<Engine>::values() [with Engine = lolog::Undirected]’:
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:394:27: required from ‘std::vector<double> lolog::Stat<NetworkEngine, StatEngine>::values() [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
394 | return stat.values();
| ~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:390:16: required from ‘std::vector<double> lolog::Stat<NetworkEngine, StatEngine>::vValues() [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
390 | return values();
| ^~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:389:33: required from here
389 | virtual std::vector<double> vValues(){
| ^~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:482:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
482 | for(int i=0;i<this->stats.size();i++)
| ~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h: In instantiation of ‘double lolog::BaseStat<Engine>::logLik() [with Engine = lolog::Undirected]’:
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:405:27: required from ‘double lolog::Stat<NetworkEngine, StatEngine>::logLik() [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
405 | return stat.logLik();
| ~~~~~~~~~~~^~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:401:16: required from ‘double lolog::Stat<NetworkEngine, StatEngine>::vLogLik() [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
401 | return logLik();
| ^~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:400:20: required from here
400 | virtual double vLogLik(){
| ^~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
492 | for(int i=0;i<this->stats.size();i++)
| ~^~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/lolog/include/Constraint.h:4,
from /data/gannet/ripley/R/test-dev/lolog/include/lolog.h:7:
/data/gannet/ripley/R/test-dev/lolog/include/Offset.h: In instantiation of ‘void lolog::BaseOffset<Engine>::rollback(const lolog::BinaryNet<Engine>&) [with Engine = lolog::Undirected]’:
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:302:22: required from ‘void lolog::Stat<NetworkEngine, StatEngine>::rollback(const lolog::BinaryNet<Engine>&) [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
302 | stat.rollback(net);
| ~~~~~~~~~~~~~^~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:298:9: required from ‘void lolog::Stat<NetworkEngine, StatEngine>::vRollback(const lolog::BinaryNet<Engine>&) [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
298 | rollback(net);
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:297:18: required from here
297 | virtual void vRollback(const BinaryNet<NetworkEngine>& net){
| ^~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Offset.h:422:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
422 | for(int i=0;i<stats.size();i++){
| ~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Offset.h: In instantiation of ‘void lolog::BaseOffset<Engine>::resetLastStats() [with Engine = lolog::Undirected]’:
/data/gannet/ripley/R/test-dev/lolog/include/Offset.h:388:9: required from ‘void lolog::BaseOffset<Engine>::discreteVertexUpdate(const lolog::BinaryNet<Engine>&, const int&, const int&, const int&, const std::vector<int>&, const int&) [with Engine = lolog::Undirected]’
388 | resetLastStats();
| ^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:269:34: required from ‘void lolog::Stat<NetworkEngine, StatEngine>::discreteVertexUpdate(const lolog::BinaryNet<Engine>&, const int&, const int&, const int&, const std::vector<int>&, const int&) [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
269 | stat.discreteVertexUpdate(net,vert,variable,newValue,order,actorIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:264:9: required from ‘void lolog::Stat<NetworkEngine, StatEngine>::vDiscreteVertexUpdate(const lolog::BinaryNet<Engine>&, const int&, const int&, const int&, const std::vector<int>&, const int&) [with NetworkEngine = lolog::Undirected; StatEngine = lologext::MinTriadicClosure<lolog::Undirected>]’
264 | discreteVertexUpdate(net,vert,variable,newValue,order,actorIndex);
| ^~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Stat.h:262:18: required from here
262 | virtual void vDiscreteVertexUpdate(const BinaryNet<NetworkEngine>& net, const int& vert,
| ^~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/lolog/include/Offset.h:416:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
416 | for(int i=0;i<stats.size();i++){
| ~^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/lolog/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/lolog/include' -I'/data/gannet/ripley/R/test-dev/BH/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 init.cpp -o init.o
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o MinTriadic.so MinTriadicClosure.o RcppExports.o init.o
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/MinTriadic/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/MinTriadic/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/MinTriadic/src'
installing to /data/gannet/ripley/R/packages/tests-devel/MinTriadic.Rcheck/00LOCK-MinTriadic/00new/MinTriadic/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 (MinTriadic)