* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘TDA’ ...
** package ‘TDA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/bin/sh: 1: clang++: not found
expr: syntax error: unexpected argument ‘50000’
/bin/sh: 1: clang++: not found
expr: syntax error: unexpected argument ‘110003’
using C++ compiler: ‘Debian clang version 19.1.5 (1)’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9h8ab6/R.INSTALL3a70b450229416/TDA/src'
/bin/sh: 1: clang++: not found
expr: syntax error: unexpected argument ‘50000’
/bin/sh: 1: clang++: not found
expr: syntax error: unexpected argument ‘110003’
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -DCGAL_DO_NOT_USE_BOOST_MP -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -DCGAL_DO_NOT_USE_BOOST_MP -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c diag.cpp -o diag.o
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:5:
In file included from ./topology/rips.h:6:
In file included from ./topology/simplex.h:221:
./topology/simplex.hpp:12:1: warning: 'BoundaryIterator' defined as a struct here but previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
12 | struct Simplex<V,T>::BoundaryIterator: public boost::iterator_adaptor<BoundaryIterator, // Derived
| ^
./topology/simplex.h:47:9: note: did you mean struct here?
47 | class BoundaryIterator;
| ^~~~~
| struct
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:5:
./topology/rips.h:173:1: warning: 'ComparePair' defined as a struct here but previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
173 | struct Rips<Distances_, Simplex_>::ComparePair
| ^
./topology/rips.h:35:9: note: did you mean struct here?
35 | class ComparePair;
| ^~~~~
| struct
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:8:
In file included from ./topology/dynamic-persistence.h:7:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages]
36 | BOOST_PRAGMA_MESSAGE(
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^
<scratch space>:83:2: note: expanded from here
83 | message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.")
| ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:9:
In file included from ./topology/persistence-diagram.h:176:
In file included from ./topology/persistence-diagram.hpp:143:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<boost::no_property>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) noexcept : px( p.release() )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:408:18: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
408 | property_ptr m_property;
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/graph_traits.hpp:61:22: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>' requested here
61 | typedef typename G::vertex_descriptor vertex_descriptor;
| ^
./topology/persistence-diagram.hpp:163:40: note: in instantiation of template class 'boost::graph_traits<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS>>' requested here
163 | typedef std::vector<boost::graph_traits<Graph>::vertex_descriptor> MatchingVector;
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
| ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:9:
In file included from ./topology/persistence-diagram.h:176:
In file included from ./topology/persistence-diagram.hpp:143:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<boost::archive::detail::basic_oarchive_impl>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) noexcept : px( p.release() )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/archive/detail/basic_oarchive.hpp:49:44: note: in instantiation of template class 'boost::scoped_ptr<boost::archive::detail::basic_oarchive_impl>' requested here
49 | boost::scoped_ptr<basic_oarchive_impl> pimpl;
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::archive::detail::basic_oarchive_impl>' has been explicitly marked deprecated here
291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
| ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:9:
In file included from ./topology/persistence-diagram.h:176:
In file included from ./topology/persistence-diagram.hpp:143:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/graph/adjacency_list.hpp:22:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/scoped_ptr.hpp:13:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: 'auto_ptr<boost::archive::detail::basic_iarchive_impl>' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) noexcept : px( p.release() )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/archive/detail/basic_iarchive.hpp:51:44: note: in instantiation of template class 'boost::scoped_ptr<boost::archive::detail::basic_iarchive_impl>' requested here
51 | boost::scoped_ptr<basic_iarchive_impl> pimpl;
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward/auto_ptr.h:291:7: note: 'auto_ptr<boost::archive::detail::basic_iarchive_impl>' has been explicitly marked deprecated here
291 | } _GLIBCXX11_DEPRECATED_SUGGEST("std::unique_ptr");
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:108:45: note: expanded from macro '_GLIBCXX11_DEPRECATED_SUGGEST'
108 | # define _GLIBCXX11_DEPRECATED_SUGGEST(ALT) _GLIBCXX_DEPRECATED_SUGGEST(ALT)
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14/bits/c++config.h:100:19: note: expanded from macro '_GLIBCXX_DEPRECATED_SUGGEST'
100 | __attribute__ ((__deprecated__ ("use '" ALT "' instead")))
| ^
In file included from diag.cpp:13:
./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 diag.cpp:16:
./tdautils/typecastUtils.h:350:12: warning: unused variable 'iFill' [-Wunused-variable]
350 | unsigned iFill = 0;
| ^~~~~
./tdautils/typecastUtils.h:394:12: warning: unused variable 'iFill' [-Wunused-variable]
394 | unsigned iFill = 0;
| ^~~~~
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:10:
In file included from ./gudhi/Simplex_tree.h:15:
In file included from ./gudhi/Simplex_tree/Simplex_tree_siblings.h:16:
In file included from ./boost/container/flat_map.hpp:29:
In file included from ./boost/container/detail/flat_tree.hpp:30:
./boost/container/vector.hpp:3173:1: error: unknown type name 'BOOST_MOVE_STD_NS_BEG'
3173 | BOOST_MOVE_STD_NS_BEG
| ^
./boost/container/vector.hpp:3175:1: error: expected unqualified-id
3175 | template <class Pointer, bool IsConst>
| ^
./boost/container/vector.hpp:3180:1: error: unknown type name 'BOOST_MOVE_STD_NS_END'
3180 | BOOST_MOVE_STD_NS_END
| ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:10:
In file included from ./gudhi/Simplex_tree.h:15:
In file included from ./gudhi/Simplex_tree/Simplex_tree_siblings.h:16:
In file included from ./boost/container/flat_map.hpp:29:
In file included from ./boost/container/detail/flat_tree.hpp:37:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/container/detail/is_sorted.hpp:21:1: error: expected unqualified-id
21 | namespace boost {
| ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:10:
In file included from ./gudhi/Simplex_tree.h:15:
In file included from ./gudhi/Simplex_tree/Simplex_tree_siblings.h:16:
In file included from ./boost/container/flat_map.hpp:29:
./boost/container/detail/flat_tree.hpp:148:38: error: no template named 'back_free_capacity'
148 | (braw, iraw, eraw, comp, eraw, back_free_capacity<SequenceContainer>::get(dest));
| ^
./boost/container/detail/flat_tree.hpp:175:32: error: no template named 'back_free_capacity'
175 | (iraw, eraw, comp, eraw, back_free_capacity<SequenceContainer>::get(dest));
| ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:26:
In file included from ./CGAL/Delaunay_triangulation.h:15:
In file included from ./CGAL/license/Triangulation.h:17:
./CGAL/config.h:124:9: warning: 'BOOST_PARAMETER_MAX_ARITY' macro redefined [-Wmacro-redefined]
124 | #define BOOST_PARAMETER_MAX_ARITY 12
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/parameter/config.hpp:61:9: note: previous definition is here
61 | #define BOOST_PARAMETER_MAX_ARITY BOOST_MPL_LIMIT_VECTOR_SIZE
| ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:17:
In file included from ./tdautils/cgalUtils.h:1:
In file included from ./CGAL/Exact_predicates_inexact_constructions_kernel.h:20:
In file included from ./CGAL/Simple_cartesian.h:20:
In file included from ./CGAL/Cartesian/Cartesian_base.h:62:
In file included from ./CGAL/Cartesian/function_objects.h:20:
In file included from ./CGAL/Kernel/function_objects.h:29:
In file included from ./CGAL/intersection_3.h:31:
In file included from ./CGAL/Intersections_3/Bbox_3_Tetrahedron_3.h:20:
In file included from ./CGAL/Intersections_3/internal/Tetrahedron_3_Bounded_3_do_intersect.h:20:
In file included from ./CGAL/Intersections_3/Triangle_3_Triangle_3.h:19:
./CGAL/Intersections_3/internal/Triangle_3_Triangle_3_intersection.h:52:7: warning: variable 'pt_added' set but not used [-Wunused-but-set-variable]
52 | int pt_added=0;
| ^
In file included from diag.cpp:19:
./tdautils/gudhiUtils.h:241:28: warning: variable 'count_vertices' set but not used [-Wunused-but-set-variable]
241 | Alpha_shape_3::size_type count_vertices = 0;
| ^
./tdautils/gudhiUtils.h:242:28: warning: variable 'count_edges' set but not used [-Wunused-but-set-variable]
242 | Alpha_shape_3::size_type count_edges = 0;
| ^
./tdautils/gudhiUtils.h:243:28: warning: variable 'count_facets' set but not used [-Wunused-but-set-variable]
243 | Alpha_shape_3::size_type count_facets = 0;
| ^
./tdautils/gudhiUtils.h:244:28: warning: variable 'count_cells' set but not used [-Wunused-but-set-variable]
244 | Alpha_shape_3::size_type count_cells = 0;
| ^
In file included from diag.cpp:34:
./kde.h:21:16: warning: unused variable 'pi' [-Wunused-variable]
21 | const double pi = 3.141592653589793;
| ^~
17 warnings and 6 errors generated.
make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:202: diag.o] Error 1
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9h8ab6/R.INSTALL3a70b450229416/TDA/src'
ERROR: compilation failed for package ‘TDA’
* removing ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TDA’