* installing *source* package ‘TDA’ ... ** package ‘TDA’ successfully unpacked and MD5 sums checked ** using staged installation ** libs expr: syntax error: unexpected argument ‘110003’ using C++ compiler: ‘clang version 18.1.4’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/TDA/src' expr: syntax error: unexpected argument ‘110003’ /usr/local/clang18/bin/clang++ -std=gnu++17 -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/clang18/include -I/usr/local/clang/include -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -DCGAL_DO_NOT_USE_BOOST_MP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang18/bin/clang++ -std=gnu++17 -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/clang18/include -I/usr/local/clang/include -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -DCGAL_DO_NOT_USE_BOOST_MP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c diag.cpp -o diag.o 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:29: 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:61: /data/gannet/ripley/R/test-clang/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 /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:29: 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/SparseLU:35: /data/gannet/ripley/R/test-clang/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 | ^ /data/gannet/ripley/R/test-clang/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 /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/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/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 /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:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/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; | ^ 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::BoundaryIterator: public boost::iterator_adaptor::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: /data/gannet/ripley/R/test-clang/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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] 36 | BOOST_PRAGMA_MESSAGE( | ^ /data/gannet/ripley/R/test-clang/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))) | ^ :74:2: note: expanded from here 74 | message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") | ^ 5 warnings generated. 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: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 | ^ /data/gannet/ripley/R/test-clang/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; | ^~ 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] 60 | 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] 45 | using Point = Kernel::Point_d; | ^ 16 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/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' expr: syntax error: unexpected argument ‘110003’ 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)