* installing *source* package ‘TDA’ ...
** package ‘TDA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/TDA/src'
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang/include  -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic  -g -O3 -Wall -pedantic -frtti  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang/include  -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic  -g -O3 -Wall -pedantic -frtti  -c diag.cpp -o diag.o
In file included from diag.cpp:6:
In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
In file included from /data/gannet/ripley/R/test-clang/Rcpp/include/RcppCommon.h:128:
/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:1:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Core:535:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:2:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/LU:47:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:12:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Jacobi:29:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:43:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/QR:17:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Householder:27:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:5:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SVD:48:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:6:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Geometry:58:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:58:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:66:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:71:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCholesky:43:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:32:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseQR:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:33:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/CholmodSupport:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:35:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:39:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:40:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
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:
In file included from ./topology/simplex.hpp:3:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/serialization/set.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/archive/detail/basic_iarchive.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::archive::detail::basic_iarchive_impl>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/data/gannet/ripley/R/test-clang/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
    boost::scoped_ptr<basic_iarchive_impl> pimpl;
                                           ^
/usr/local/bin/../include/c++/v1/memory:2079:28: note: 'auto_ptr<boost::archive::detail::basic_iarchive_impl>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/usr/local/bin/../include/c++/v1/__config:944:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/local/bin/../include/c++/v1/__config:933:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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]
struct Simplex<V,T>::BoundaryIterator: public boost::iterator_adaptor<BoundaryIterator,                                 // Derived
^
./topology/simplex.h:47:9: note: did you mean struct here?
        class BoundaryIterator;
        ^~~~~
        struct
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:5:
./topology/rips.h:158:1: 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]
struct Rips<Distances_, Simplex_>::ComparePair: 
^
./topology/rips.h:35:9: note: did you mean struct here?
        class               ComparePair;       
        ^~~~~
        struct
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:
In file included from ./topology/simplex.hpp:3:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/serialization/set.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/archive/detail/basic_iarchive.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::no_property>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/adjacency_list.hpp:363:19: note: in instantiation of template class 'boost::scoped_ptr<boost::no_property>' requested here
    property_ptr  m_property;
                  ^
/data/gannet/ripley/R/test-clang/BH/include/boost/graph/graph_traits.hpp:57:26: note: in instantiation of template class 'boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::no_property, boost::no_property, boost::no_property, boost::listS>' requested here
        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, boost::no_property, boost::no_property, boost::no_property, boost::listS> >' requested here
    typedef         std::vector<boost::graph_traits<Graph>::vertex_descriptor>                  MatchingVector;
                                       ^
/usr/local/bin/../include/c++/v1/memory:2079:28: note: 'auto_ptr<boost::no_property>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/usr/local/bin/../include/c++/v1/__config:944:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/local/bin/../include/c++/v1/__config:933:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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:
In file included from ./topology/simplex.hpp:3:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/serialization/set.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/archive/detail/basic_iarchive.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/scoped_ptr.hpp:13:
/data/gannet/ripley/R/test-clang/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'auto_ptr<boost::archive::detail::basic_oarchive_impl>' is deprecated [-Wdeprecated-declarations]
    explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                              ^
/data/gannet/ripley/R/test-clang/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
    boost::scoped_ptr<basic_oarchive_impl> pimpl;
                                           ^
/usr/local/bin/../include/c++/v1/memory:2079:28: note: 'auto_ptr<boost::archive::detail::basic_oarchive_impl>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/usr/local/bin/../include/c++/v1/__config:944:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/local/bin/../include/c++/v1/__config:933:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
17 warnings generated.
In file included from diag.cpp:13:
./tdautils/gridUtils.h:183:13: warning: unused variable 'value' [-Wunused-variable]
     double value, value2;  // max of value and value 2 is the fcn value. 
            ^
./tdautils/gridUtils.h:183:20: warning: unused variable 'value2' [-Wunused-variable]
     double value, value2;  // max of value and value 2 is the fcn value. 
                   ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:36:
In file included from ./CGAL/Delaunay_triangulation.h:24:
In file included from ./CGAL/license/Triangulation.h:27:
./CGAL/config.h:119:9: warning: 'BOOST_PARAMETER_MAX_ARITY' macro redefined [-Wmacro-redefined]
#define BOOST_PARAMETER_MAX_ARITY 12
        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/parameter/config.hpp:10:10: note: previous definition is here
# define BOOST_PARAMETER_MAX_ARITY 8
         ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:36:
In file included from ./CGAL/Delaunay_triangulation.h:29:
In file included from ./CGAL/Triangulation.h:29:
In file included from ./CGAL/Triangulation_data_structure.h:32:
In file included from ./CGAL/Triangulation_face.h:29:
In file included from ./CGAL/internal/Static_or_dynamic_array.h:28:
In file included from ./CGAL/Dimension.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Core:535:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:36:
In file included from ./CGAL/Delaunay_triangulation.h:29:
In file included from ./CGAL/Triangulation.h:33:
In file included from ./CGAL/spatial_sort.h:26:
In file included from ./CGAL/hilbert_sort.h:28:
In file included from ./CGAL/Hilbert_sort_2.h:25:
In file included from ./CGAL/Hilbert_sort_median_2.h:27:
In file included from ./CGAL/Hilbert_sort_base.h:26:
In file included from ./CGAL/algorithm.h:39:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/random.hpp:36:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/random/additive_combine.hpp:27:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/random/detail/integer_log2.hpp:19:
/data/gannet/ripley/R/test-clang/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:92:2: note: expanded from here
 message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
 ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_base.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_LA_base.h:37:
In file included from ./CGAL/NewKernel_d/LA_eigen/LA.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:2:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/LU:47:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_base.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_LA_base.h:37:
In file included from ./CGAL/NewKernel_d/LA_eigen/LA.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:12:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Jacobi:29:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_base.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_LA_base.h:37:
In file included from ./CGAL/NewKernel_d/LA_eigen/LA.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:43:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_base.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_LA_base.h:37:
In file included from ./CGAL/NewKernel_d/LA_eigen/LA.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:4:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/QR:17:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Householder:27:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_base.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_LA_base.h:37:
In file included from ./CGAL/NewKernel_d/LA_eigen/LA.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:5:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SVD:48:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_base.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_LA_base.h:37:
In file included from ./CGAL/NewKernel_d/LA_eigen/LA.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:6:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Geometry:58:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_base.h:26:
In file included from ./CGAL/NewKernel_d/Cartesian_LA_base.h:37:
In file included from ./CGAL/NewKernel_d/LA_eigen/LA.h:30:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:58:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:13:
In file included from ./gudhi/Alpha_complex.h:37:
In file included from ./CGAL/Epick_d.h:27:
In file included from ./CGAL/NewKernel_d/Cartesian_static_filters.h:26:
In file included from ./CGAL/internal/Static_filters/Orientation_2.h:27:
./CGAL/internal/Static_filters/Static_filter_error.h:125:11: warning: unused variable 'e' [-Wunused-variable]
      Sfe e = *this + f;
          ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:16:
In file included from ./tdautils/cgalUtils.h:1:
In file included from ./CGAL/Exact_predicates_inexact_constructions_kernel.h:30:
In file included from ./CGAL/Filtered_kernel.h:37:
In file included from ./CGAL/internal/Static_filters/Static_filters.h:73:
./CGAL/internal/Static_filters/Do_intersect_3.h:306:7: warning: unused variable 'f1bis' [-Wunused-variable]
    F f1bis = (t1 - t1) - (t1 - t1);
      ^
./CGAL/internal/Static_filters/Do_intersect_3.h:308:7: warning: unused variable 'f3' [-Wunused-variable]
    F f3 = f2 - f2;
      ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:16:
In file included from ./tdautils/cgalUtils.h:2:
In file included from ./CGAL/Delaunay_triangulation_3.h:34:
In file included from ./CGAL/Triangulation_3.h:47:
./CGAL/Triangulation_data_structure_3.h:3439:7: warning: use of the 'fallthrough' attribute is a C++17 extension [-Wc++17-extensions]
      CGAL_FALLTHROUGH;
      ^
./CGAL/config.h:637:30: note: expanded from macro 'CGAL_FALLTHROUGH'
#  define CGAL_FALLTHROUGH [[fallthrough]]
                             ^
In file included from diag.cpp:34:
./kde.h:21:16: warning: unused variable 'pi' [-Wunused-variable]
  const double pi = 3.141592653589793;
               ^
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:36:63: warning: 'bind2nd<std::__1::not_equal_to<unsigned int>, unsigned int>' is deprecated [-Wdeprecated-declarations]
            return      Self(boost::make_filter_iterator(std::bind2nd(NotEqualVertex(), *(this->base())), vertices_.begin(), vertices_.end()),
                                                              ^
/data/gannet/ripley/R/test-clang/BH/include/boost/iterator/iterator_facade.hpp:550:20: note: in instantiation of member function 'Simplex<unsigned int, double>::BoundaryIterator::dereference' requested here
          return f.dereference();
                   ^
/data/gannet/ripley/R/test-clang/BH/include/boost/iterator/iterator_facade.hpp:656:42: note: in instantiation of function template specialization 'boost::iterators::iterator_core_access::dereference<Simplex<unsigned int, double>::BoundaryIterator>' requested here
            return iterator_core_access::dereference(this->derived());
                                         ^
/data/gannet/ripley/R/test-clang/BH/include/boost/foreach.hpp:771:12: note: in instantiation of member function 'boost::iterators::detail::iterator_facade_base<Simplex<unsigned int, double>::BoundaryIterator, Simplex<unsigned int, double>, boost::iterators::random_access_traversal_tag, Simplex<unsigned int, double>, long, false, false>::operator*' requested here
    return *auto_any_cast<iter_t, boost::mpl::false_>(cur);
           ^
./topology/static-persistence.hpp:34:9: note: in instantiation of function template specialization 'boost::foreach_detail_::deref<std::__1::pair<Simplex<unsigned int, double>::BoundaryIterator, Simplex<unsigned int, double>::BoundaryIterator>, mpl_::bool_<true> >' requested here
        BOOST_FOREACH(const typename Filtration::Simplex& s, std::make_pair(cur->boundary_begin(), cur->boundary_end()))
        ^
/data/gannet/ripley/R/test-clang/BH/include/boost/foreach.hpp:1107:20: note: expanded from macro 'BOOST_FOREACH'
        for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
                   ^
/data/gannet/ripley/R/test-clang/BH/include/boost/foreach.hpp:1040:29: note: expanded from macro 'BOOST_FOREACH_DEREF'
    boost::foreach_detail_::deref(                                                              \
                            ^
./topology/static-persistence.h:95:99: note: in instantiation of function template specialization 'StaticPersistence<Empty<void>, VectorChains<int>, OrderContainer<Empty<void> >, PairCycleData<Empty<void>, VectorChains<int>, use_default>, ElementComparison<boost::multi_index::multi_index_container<PairCycleData<Empty<void>, VectorChains<int>, use_default>, boost::multi_index::indexed_by<boost::multi_index::random_access<boost::multi_index::tag<order, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::__1::allocator<PairCycleData<Empty<void>, VectorChains<int>, use_default> > >, std::__1::greater<boost::multi_index::detail::rnd_node_iterator<boost::multi_index::detail::random_access_index_node<boost::multi_index::detail::index_node_base<PairCycleData<Empty<void>, VectorChains<int>, use_default>, std::__1::allocator<PairCycleData<Empty<void>, VectorChains<int>, use_default> > > > > > > >::initialize<Filtration<Simplex<unsigned int, double>, boost::multi_index::ordered_unique<boost::multi_index::identity<Simplex<unsigned int, double> >, Simplex<unsigned int, double>::VertexComparison, mpl_::na> > >' requested here
        template<class Filtration>      StaticPersistence(const Filtration& f): ocmp_(order_)   { initialize(f); }
                                                                                                  ^
./tdautils/dionysusUtils.h:246:14: note: in instantiation of function template specialization 'StaticPersistence<Empty<void>, VectorChains<int>, OrderContainer<Empty<void> >, PairCycleData<Empty<void>, VectorChains<int>, use_default>, ElementComparison<boost::multi_index::multi_index_container<PairCycleData<Empty<void>, VectorChains<int>, use_default>, boost::multi_index::indexed_by<boost::multi_index::random_access<boost::multi_index::tag<order, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::__1::allocator<PairCycleData<Empty<void>, VectorChains<int>, use_default> > >, std::__1::greater<boost::multi_index::detail::rnd_node_iterator<boost::multi_index::detail::random_access_index_node<boost::multi_index::detail::index_node_base<PairCycleData<Empty<void>, VectorChains<int>, use_default>, std::__1::allocator<PairCycleData<Empty<void>, VectorChains<int>, use_default> > > > > > > >::StaticPersistence<Filtration<Simplex<unsigned int, double>, boost::multi_index::ordered_unique<boost::multi_index::identity<Simplex<unsigned int, double> >, Simplex<unsigned int, double>::VertexComparison, mpl_::na> > >' requested here
        Persistence p(filtration); // initialize persistence
                    ^
./tdautils/filtrationDiag.h:68:5: note: in instantiation of function template specialization 'FiltrationDiagDionysus<StaticPersistence<Empty<void>, VectorChains<int>, OrderContainer<Empty<void> >, PairCycleData<Empty<void>, VectorChains<int>, use_default>, ElementComparison<boost::multi_index::multi_index_container<PairCycleData<Empty<void>, VectorChains<int>, use_default>, boost::multi_index::indexed_by<boost::multi_index::random_access<boost::multi_index::tag<order, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::__1::allocator<PairCycleData<Empty<void>, VectorChains<int>, use_default> > >, std::__1::greater<boost::multi_index::detail::rnd_node_iterator<boost::multi_index::detail::random_access_index_node<boost::multi_index::detail::index_node_base<PairCycleData<Empty<void>, VectorChains<int>, use_default>, std::__1::allocator<PairCycleData<Empty<void>, VectorChains<int>, use_default> > > > > > > >, Filtration<Simplex<unsigned int, double>, boost::multi_index::ordered_unique<boost::multi_index::identity<Simplex<unsigned int, double> >, Simplex<unsigned int, double>::VertexComparison, mpl_::na> > >' requested here
    FiltrationDiagDionysus< Persistence >(
    ^
./grid.h:148:3: note: in instantiation of function template specialization 'filtrationDiagSorted<std::__1::vector<unsigned int, std::__1::allocator<unsigned int> >, std::__1::vector<std::__1::vector<unsigned int, std::__1::allocator<unsigned int> >, std::__1::allocator<std::__1::vector<unsigned int, std::__1::allocator<unsigned int> > > >, std::__1::vector<double, std::__1::allocator<double> > >' requested here
  filtrationDiagSorted< VertexVector >(
  ^
diag.cpp:127:3: note: in instantiation of function template specialization 'gridDiag<std::__1::vector<unsigned int, std::__1::allocator<unsigned int> >, Rcpp::Vector<14, PreserveStorage>, Rcpp::Vector<13, PreserveStorage>, void (const char *, ...)>' requested here
  gridDiag< std::vector< unsigned > >(
  ^
/usr/local/bin/../include/c++/v1/functional:1082:1: note: 'bind2nd<std::__1::not_equal_to<unsigned int>, unsigned int>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/usr/local/bin/../include/c++/v1/__config:944:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/local/bin/../include/c++/v1/__config:933:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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:37:63: warning: 'bind2nd<std::__1::not_equal_to<unsigned int>, unsigned int>' is deprecated [-Wdeprecated-declarations]
                             boost::make_filter_iterator(std::bind2nd(NotEqualVertex(), *(this->base())), vertices_.end(),   vertices_.end()));
                                                              ^
/usr/local/bin/../include/c++/v1/functional:1082:1: note: 'bind2nd<std::__1::not_equal_to<unsigned int>, unsigned int>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/usr/local/bin/../include/c++/v1/__config:944:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/local/bin/../include/c++/v1/__config:933:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from diag.cpp:19:
In file included from ./tdautils/gudhiUtils.h:10:
./gudhi/Simplex_tree.h:1184:64: warning: lambda capture 'this' is not used [-Wunused-lambda-capture]
                                                              [this](Simplex_handle sh1, Simplex_handle sh2) {
                                                               ^
./gudhi/Simplex_tree.h:1163:21: note: in instantiation of member function 'Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>::rec_make_filtration_non_decreasing' requested here
        modified |= rec_make_filtration_non_decreasing(simplex.second.children());
                    ^
./gudhi/Alpha_complex.h:343:26: note: in instantiation of member function 'Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>::make_filtration_non_decreasing' requested here
    bool modified_filt = make_filtration_non_decreasing();
                         ^
./gudhi/Alpha_complex.h:222:7: note: in instantiation of member function 'Gudhi::alphacomplex::Alpha_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> >::init' requested here
      init(max_alpha_square);
      ^
./gudhi/Alpha_complex.h:165:5: note: in instantiation of function template specialization 'Gudhi::alphacomplex::Alpha_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> >::init_from_range<std::__1::list<CGAL::Wrap::Point_d<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> >, std::__1::allocator<CGAL::Wrap::Point_d<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> > > > >' requested here
    init_from_range(points, max_alpha_square);
    ^
./tdautils/gudhiUtils.h:366:3: note: in instantiation of function template specialization 'Gudhi::alphacomplex::Alpha_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> >::Alpha_complex<std::__1::list<CGAL::Wrap::Point_d<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> >, std::__1::allocator<CGAL::Wrap::Point_d<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> > > > >' requested here
                alpha_complex_from_points(lp, std::numeric_limits<double>::infinity());
                ^
diag.cpp:469:7: note: in instantiation of function template specialization 'AlphaComplexFiltrationGudhi<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>, Rcpp::Matrix<14, PreserveStorage>, void (const char *, ...)>' requested here
      AlphaComplexFiltrationGudhi< Gudhi::Simplex_tree<> >(
      ^
In file included from diag.cpp:9:
In file included from ./tdautils/ripsL2.h:8:
In file included from ./topology/dynamic-persistence.h:332:
./topology/dynamic-persistence.hpp:60:73: warning: unused typedef 'TrailIterator' [-Wunused-local-typedef]
    typedef                 typename Element::Trail::iterator           TrailIterator;
                                                                        ^
In file included from diag.cpp:30:
./alphaComplex.h:45:9: warning: unused type alias 'Point' [-Wunused-local-typedef]
  using Point = Kernel::Point_d;
        ^
28 warnings generated.
clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o TDA.so RcppExports.o diag.o -lgmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/TDA/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/TDA/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/TDA/src'
installing to /data/gannet/ripley/R/packages/tests-clang/TDA.Rcheck/00LOCK-TDA/00new/TDA/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 (TDA)