* installing *source* package ‘TDA’ ...
** package ‘TDA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
expr: syntax error
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
expr: syntax error
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I/opt/R/x86_64/include -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I/opt/R/x86_64/include -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fPIC -falign-functions=64 -Wall -g -O2 -c diag.cpp -o diag.o
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Index count = 0;
^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
Index nsuper_et = 0; // Number of relaxed snodes in the original etree
^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
Index replacements = 0;
^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
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: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]
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:8:
In file included from ./topology/dynamic-persistence.h:7:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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]
BOOST_PRAGMA_MESSAGE(
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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>:168:2: note: expanded from here
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: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:16:
./tdautils/typecastUtils.h:350:12: warning: unused variable 'iFill' [-Wunused-variable]
unsigned iFill = 0;
^
./tdautils/typecastUtils.h:394:12: warning: unused variable 'iFill' [-Wunused-variable]
unsigned iFill = 0;
^
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]
#define BOOST_PARAMETER_MAX_ARITY 12
^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include/boost/parameter/config.hpp:61:9: note: previous definition is here
#define BOOST_PARAMETER_MAX_ARITY BOOST_MPL_LIMIT_VECTOR_SIZE
^
5 warnings generated.
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]
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]
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]
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]
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]
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]
const double pi = 3.141592653589793;
^
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;
^
16 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o TDA.so RcppExports.o diag.o -lgmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
expr: syntax error
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/TDA.Rcheck/00LOCK-TDA/00new/TDA/libs
** generating debug symbols (dSYM)
** 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)