* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘LOMAR’ ...
** package ‘LOMAR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/tmp/RtmpWHcRYg/R.INSTALL7989668f1dab8/LOMAR/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DBOOST_DISABLE_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DBOOST_DISABLE_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -c diag.cpp -o diag.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/iterator/advance.hpp:12,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/next_prior.hpp:24,
from ./tdautils/ripsL2.h:3,
from diag.cpp:9:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/property_map/property_map.hpp:598,
from ./utilities/property-maps.h:6,
from ./topology/complex-traits.h:6,
from ./topology/filtration.h:7,
from ./tdautils/ripsL2.h:6:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/memory:78,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/shared_count.hpp:27:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:25,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/bind/bind.hpp:26,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/multi_index/detail/ord_index_impl.hpp:82,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/multi_index/ordered_index.hpp:17,
from ./topology/filtration.h:14:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/get_pointer.hpp: At global scope:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./topology/dynamic-persistence.h:332,
from ./tdautils/ripsL2.h:8:
./topology/dynamic-persistence.hpp: In member function ‘bool DynamicPersistenceTrails<Data_, ChainTraits_, ContainerTraits_, Element_, Comparison_, ConsistencyComparison_>::transpose(iterator, const DimensionFunctor&, Visitor)’:
./topology/dynamic-persistence.hpp:60:73: warning: typedef ‘TrailIterator’ locally defined but not used [-Wunused-local-typedefs]
60 | typedef typename Element::Trail::iterator TrailIterator;
| ^~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22,
from ./topology/persistence-diagram.hpp:143,
from ./topology/persistence-diagram.h:176,
from ./tdautils/ripsL2.h:9:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from diag.cpp:26:
./kde.h: In instantiation of ‘RealVector kde(const RealMatrix&, const RealMatrix&, unsigned int, unsigned int, unsigned int, double, const std::string&, const RealVector&, bool, const Print&) [with RealVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; RealMatrix = Rcpp::Matrix<14>; Print = void(const char*, ...); std::string = std::__cxx11::basic_string<char>]’:
diag.cpp:166:13: required from here
166 | return kde(
| ~~~^
167 | X, Grid, X.nrow(), Grid.ncol(), Grid.nrow(), h, kertype, weight,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
168 | printProgress, Rprintf);
| ~~~~~~~~~~~~~~~~~~~~~~~
./kde.h:21:16: warning: unused variable ‘pi’ [-Wunused-variable]
21 | const double pi = 3.141592653589793;
| ^~
In file included from diag.cpp:13:
./tdautils/gridUtils.h: In instantiation of ‘void addOddTets(int, int, int, int, int, VectorList&) [with VectorList = std::vector<std::vector<unsigned int> >]’:
./tdautils/gridUtils.h:315:14: required from ‘void addAllTetrahedra(int, int, int, int, int, VectorList&) [with VectorList = std::vector<std::vector<unsigned int> >]’
315 | addOddTets(ncols, nrows, i, j, k, cmplx);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./tdautils/gridUtils.h:363:20: required from ‘void simplicesFromGrid(const DimensionVector&, int, VectorList&) [with DimensionVector = Rcpp::Vector<13>; VectorList = std::vector<std::vector<unsigned int> >]’
363 | addAllTetrahedra(ncols, nrows, i, j, k, cmplx);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./grid.h:90:22: required from ‘void gridFiltration(const RealVector&, const DimensionVector&, int, const std::string&, bool, const Print&, std::vector<ValueT>&, std::vector<double>&) [with RealVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; DimensionVector = Rcpp::Vector<13>; Print = void(const char*, ...); VertexVector = std::vector<unsigned int>; std::string = std::__cxx11::basic_string<char>]’
90 | simplicesFromGrid(gridDim, maxdimension + 1, cmplx);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diag.cpp:68:17: required from here
68 | gridFiltration(
| ~~~~~~~~~~~~~~^
69 | FUNvalues, gridDim, maxdimension, decomposition, printProgress, Rprintf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | cmplx, values);
| ~~~~~~~~~~~~~~
./tdautils/gridUtils.h:183:13: warning: unused variable ‘value’ [-Wunused-variable]
183 | double value, value2; // max of value and value 2 is the fcn value.
| ^~~~~
./tdautils/gridUtils.h:183:20: warning: unused variable ‘value2’ [-Wunused-variable]
183 | double value, value2; // max of value and value 2 is the fcn value.
| ^~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R.h:73,
from diag.cpp:2:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include/R_ext/Error.h:100:17: warning: infinite recursion detected [-Winfinite-recursion]
100 | #define warning Rf_warning
| ^~~~~~~~~~
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro ‘warning’
46 | inline void warning(const char* fmt, Args&&... args ) {
| ^~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions.h:180,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:130,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
from diag.cpp:6:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call
47 | Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o LOMAR.so RcppExports.o diag.o -lgmp -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpWHcRYg/R.INSTALL7989668f1dab8/LOMAR/src'
make[1]: Entering directory '/tmp/RtmpWHcRYg/R.INSTALL7989668f1dab8/LOMAR/src'
make[1]: Leaving directory '/tmp/RtmpWHcRYg/R.INSTALL7989668f1dab8/LOMAR/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-LOMAR/00new/LOMAR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LOMAR)