* installing *source* package ‘smer’ ... ** this is package ‘smer’ version ‘0.0.2’ ** package ‘smer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 23.1.0-rc2’ make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang-trunk/smer/src' /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c allocate_memory.cpp -o allocate_memory.o In file included from RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c check_openmp.cpp -o check_openmp.o 17 warnings generated. In file included from allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from allocate_memory.cpp:5: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c computation.cpp -o computation.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c compute_covariance_q.cpp -o compute_covariance_q.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c compute_mom_components.cpp -o compute_mom_components.o In file included from computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from computation.cpp:29: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ In file included from compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from compute_covariance_q.cpp:5: In file included from ./compute_covariance_q.h:8: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. In file included from compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from compute_mom_components.cpp:5: In file included from ./compute_mom_components.h:7: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. 17 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c count_data.cpp -o count_data.o count_data.cpp:64:7: warning: variable 'linenum' set but not used [-Wunused-but-set-variable] 64 | int linenum = 0; | ^ 1 warning generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c genotype.cpp -o genotype.o In file included from genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from genotype.cpp:29: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c hdf5_api.cpp -o hdf5_api.o In file included from hdf5_api.cpp:1: In file included from /data/localhost/ripley/R/test-clang/HighFive/include/highfive/H5Easy.hpp:58: In file included from /data/localhost/ripley/R/test-clang/HighFive/include/highfive/H5File.hpp:213: In file included from /data/localhost/ripley/R/test-clang/HighFive/include/highfive/bits/H5Node_traits_misc.hpp:26: /data/localhost/ripley/R/test-clang/HighFive/include/highfive/bits/H5Slice_traits_misc.hpp:65:48: error: no member named 'back_inserter' in namespace 'std' 65 | std::copy(vec.begin(), vec.end(), std::back_inserter(_ids)); | ^~~~~~~~~~~~~ 1 error generated. make[1]: *** [/data/localhost/ripley/R/R-clang-trunk/etc/Makeconf:197: hdf5_api.o] Error 1 /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c initialize_random_vectors.cpp -o initialize_random_vectors.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c read_covariates.cpp -o read_covariates.o In file included from initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from initialize_random_vectors.cpp:5: In file included from ./initialize_random_vectors.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c read_genotype_mask.cpp -o read_genotype_mask.o In file included from read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 read_genotype_mask.cpp:1: In file included from ./read_genotype_mask.h:2: In file included from /data/localhost/ripley/R/test-clang/HighFive/include/highfive/H5Easy.hpp:58: In file included from /data/localhost/ripley/R/test-clang/HighFive/include/highfive/H5File.hpp:213: In file included from /data/localhost/ripley/R/test-clang/HighFive/include/highfive/bits/H5Node_traits_misc.hpp:26: /data/localhost/ripley/R/test-clang/HighFive/include/highfive/bits/H5Slice_traits_misc.hpp:65:48: error: no member named 'back_inserter' in namespace 'std' 65 | std::copy(vec.begin(), vec.end(), std::back_inserter(_ids)); | ^~~~~~~~~~~~~ In file included from read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from read_covariates.cpp:1: In file included from ./read_covariates.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. In file included from read_genotype_mask.cpp:1: In file included from ./read_genotype_mask.h:5: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 read_genotype_mask.cpp:1: In file included from ./read_genotype_mask.h:5: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 read_genotype_mask.cpp:1: In file included from ./read_genotype_mask.h:5: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 read_genotype_mask.cpp:1: In file included from ./read_genotype_mask.h:5: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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; | ^ 5 warnings and 1 error generated. make[1]: *** [/data/localhost/ripley/R/R-clang-trunk/etc/Makeconf:197: read_genotype_mask.o] Error 1 /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c read_genotypes.cpp -o read_genotypes.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c read_phenotypes.cpp -o read_phenotypes.o In file included from read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from read_genotypes.cpp:1: In file included from ./read_genotypes.h:1: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. In file included from read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from read_phenotypes.cpp:1: In file included from ./read_phenotypes.h:1: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ 17 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c set_metadata.cpp -o set_metadata.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c simulate_traits.cpp -o simulate_traits.o In file included from simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from simulate_traits.cpp:1: In file included from ./simulate_traits.h:5: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ In file included from simulate_traits.cpp:1: In file included from ./simulate_traits.h:15: ./read_genotypes.h:15:22: warning: unused function template 'binary_read' [-Wunused-template] 15 | static std::istream &binary_read(std::istream &stream, T &value); | ^~~~~~~~~~~ 18 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c sme.cpp -o sme.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c test-runner.cpp -o test-runner.o In file included from sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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; | ^ /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -I/opt/homebrew/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I'/data/localhost/ripley/R/test-clang/BH/include' -I'/data/localhost/ripley/R/test-clang/HighFive/include' -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -I'/data/localhost/ripley/R/test-clang/Rhdf5lib/include' -I'/data/localhost/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c testing_utils.cpp -o testing_utils.o In file included from sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from sme.cpp:45: In file included from ./computation.h:2: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ In file included from sme.cpp:52: ./read_genotypes.h:15:22: warning: unused function template 'binary_read' [-Wunused-template] 15 | static std::istream &binary_read(std::istream &stream, T &value); | ^~~~~~~~~~~ In file included from testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/localhost/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 testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/localhost/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/localhost/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 testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/localhost/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 testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/localhost/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 testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:3: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Cholesky:32: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Cholesky/LLT.h:240:14: warning: unused function template 'llt_rank_update_lower' [-Wunused-template] 240 | static Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) | ^~~~~~~~~~~~~~~~~~~~~ In file included from testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:28: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Dense:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Eigenvalues:39: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h:839:13: warning: unused function template 'tridiagonal_qr_step' [-Wunused-template] 839 | static void tridiagonal_qr_step(RealScalar* diag, RealScalar* subdiag, Index start, Index end, Scalar* matrixQ, Index n) | ^~~~~~~~~~~~~~~~~~~ In file included from testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:55: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:18:13: warning: unused function template 'conservative_sparse_sparse_product_impl' [-Wunused-template] 18 | static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h:270:13: warning: unused function template 'sparse_sparse_to_dense_product_impl' [-Wunused-template] 270 | static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:56: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h:20:13: warning: unused function template 'sparse_sparse_product_with_pruning_impl' [-Wunused-template] 20 | static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:66: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Amd.h:35:21: warning: unused function template 'cs_wclear' [-Wunused-template] 35 | static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n) | ^~~~~~~~~ In file included from testing_utils.cpp:1: In file included from ./testing_utils.h:6: In file included from ./allocate_memory.h:8: In file included from ./genotype.h:4: In file included from ./sme.h:7: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:27: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/OrderingMethods:67: In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Ordering.h:16: /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:501:18: warning: unused function template 'init_rows_cols' [-Wunused-template] 501 | static IndexType init_rows_cols /* returns true if OK, or false otherwise */ | ^~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:717:13: warning: unused function template 'init_scoring' [-Wunused-template] 717 | static void init_scoring | ^~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:954:18: warning: unused function template 'find_ordering' [-Wunused-template] 954 | static IndexType find_ordering /* return the number of garbage collections */ | ^~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1566:13: warning: unused function template 'detect_super_cols' [-Wunused-template] 1566 | static void detect_super_cols | ^~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:1717:18: warning: unused function template 'garbage_collection' [-Wunused-template] 1717 | static IndexType garbage_collection /* returns the new value of pfree */ | ^~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/OrderingMethods/Eigen_Colamd.h:342:13: warning: unused function template 'compute_ordering' [-Wunused-template] 342 | static bool compute_ordering(IndexType n_row, IndexType n_col, IndexType Alen, IndexType *A, IndexType *p, double knobs[NKnobs], IndexType stats[NStats]) | ^~~~~~~~~~~~~~~~ In file included from testing_utils.cpp:1: In file included from ./testing_utils.h:14: ./read_genotypes.h:15:22: warning: unused function template 'binary_read' [-Wunused-template] 15 | static std::istream &binary_read(std::istream &stream, T &value); | ^~~~~~~~~~~ 18 warnings generated. 18 warnings generated. make[1]: Target 'all' not remade because of errors. make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang-trunk/smer/src' ERROR: compilation failed for package ‘smer’ * removing ‘/data/localhost/ripley/R/packages/tests-clang-trunk/smer.Rcheck/smer’