* installing to library ‘/home/hornik/tmp/R.check/r-patched-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 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprdKPVp/R.INSTALL1947402eb6b870/LOMAR/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/arg.hpp:25,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/iterator/advance.hpp:12,
                 from /home/hornik/tmp/R.check/r-patched-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-patched-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-patched-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-patched-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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/hornik/tmp/R.check/r-patched-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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from /home/hornik/tmp/R.check/r-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/bind/bind.hpp:26,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/multi_index/detail/ord_index_impl.hpp:82,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/multi_index/ordered_index.hpp:17,
                 from ./topology/filtration.h:14:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/get_pointer.hpp: At global scope:
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include/R.h:73,
                 from diag.cpp:2:
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/include/R_ext/Error.h:69:17: warning: infinite recursion detected [-Winfinite-recursion]
   69 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/exceptions.h:180,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:130,
                 from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
                 from diag.cpp:6:
/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/lib -Wl,-O1 -o LOMAR.so RcppExports.o diag.o -lgmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmprdKPVp/R.INSTALL1947402eb6b870/LOMAR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprdKPVp/R.INSTALL1947402eb6b870/LOMAR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmprdKPVp/R.INSTALL1947402eb6b870/LOMAR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-LOMAR/00new/LOMAR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘LOMAR’
    finding HTML links ... done
    GMM_Wd                                  html  
    Gaussian_Wd                             html  
    apply_transformation                    html  
    ary2ps                                  html  
    binning                                 html  
    circle_hough_transform                  html  
    coloc_index                             html  
    costWd                                  html  
    cpd                                     html  
    crop_point_set                          html  
    denoise                                 html  
    dist_to_boundary                        html  
    dist_to_line                            html  
    downsample                              html  
    find_elbow                              html  
    get_kernel_matrix                       html  
    get_persistence_diagrams                html  
    get_shape                               html  
    get_surface_area                        html  
    gradientWd                              html  
    group_events                            html  
    icp                                     html  
    idx2rowcol                              html  
    img2ps                                  html  
    jrmpc                                   html  
    local_densities                         html  
    locprec2cov                             html  
    locs2ps                                 html  
    locs_from_csv                           html  
    multiple_registration                   html  
    point_sets_from_locs                    html  
    point_sets_from_tiffs                   html  
    points2img                              html  
    points_from_roi                         html  
    ps2ary                                  html  
    pssk                                    html  
    q2dr                                    html  
    q2r                                     html  
    restore_coordinates                     html  
    rotx                                    html  
    roty                                    html  
    rotz                                    html  
    scale_alpha_shape                       html  
    shape_features_3d                       html  
    sliced_Wd                               html  
    standardize_coordinates                 html  
    tr                                      html  
    wgmmreg                                 html  
** 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)