* 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)