* installing *source* package ‘Seurat’ ... ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.5 (1)’ using C++ compiler: ‘Debian clang version 19.1.5 (1)’ using C++17 clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ModularityOptimizer.cpp -o ModularityOptimizer.o ModularityOptimizer.cpp:216:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 216 | for (; i <= nNodes; i++) | ^ ModularityOptimizer.cpp:204:3: note: previous statement is here 204 | for (size_t j = 0; j < edge[0].size(); j++) | ^ ModularityOptimizer.cpp:395:11: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 395 | k++; | ^ ModularityOptimizer.cpp:387:9: note: previous statement is here 387 | for (int l = firstNeighborIndex[node[k]]; l < firstNeighborIndex[node[k] + 1]; l++) | ^ ModularityOptimizer.cpp:399:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 399 | clustering.orderClustersByNNodes(); | ^ ModularityOptimizer.cpp:377:3: note: previous statement is here 377 | for (int i = 0; i < nNodes; i++) | ^ ModularityOptimizer.cpp:436:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 436 | subnetwork.firstNeighborIndex[i + 1] = subnetwork.nEdges; | ^ ModularityOptimizer.cpp:429:7: note: previous statement is here 429 | for (int k = firstNeighborIndex[j]; k < firstNeighborIndex[j + 1]; k++) | ^ ModularityOptimizer.cpp:721:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 721 | if (i >= 0) | ^ ModularityOptimizer.cpp:710:3: note: previous statement is here 710 | for (int j = 0; j < clustering->nClusters; j++) | ^ ModularityOptimizer.cpp:726:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 726 | if (cluster == clustering->nClusters - 1) | ^ ModularityOptimizer.cpp:723:7: note: previous statement is here 723 | for (int j = 0; j < network->nNodes; j++) | ^ ModularityOptimizer.cpp:747:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 747 | if (i >= 0) | ^ ModularityOptimizer.cpp:740:5: note: previous statement is here 740 | for (int k = 0; k < vosClusteringTechnique.clustering->nClusters; k++) | ^ ModularityOptimizer.cpp:771:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 771 | IVector firstNeighborIndex(nNodes + 1); | ^ ModularityOptimizer.cpp:764:3: note: previous statement is here 764 | for (size_t i = 0; i < node1.size(); i++) | ^ ModularityOptimizer.cpp:796:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 796 | if (modularityFunction == 1) | ^ ModularityOptimizer.cpp:783:5: note: previous statement is here 783 | for (size_t i = 0; i < node1.size(); i++) | ^ ModularityOptimizer.cpp:761:7: warning: unused variable 'n1_max' [-Wunused-variable] 761 | int n1_max = *std::max_element(node1.cbegin(), node1.cend()); | ^~~~~~ ModularityOptimizer.cpp:762:7: warning: unused variable 'n2_max' [-Wunused-variable] 762 | int n2_max = *std::max_element(node2.cbegin(), node2.cend()); | ^~~~~~ 11 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c RModularityOptimizer.cpp -o RModularityOptimizer.o In file included from RModularityOptimizer.cpp:9: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 RModularityOptimizer.cpp:9: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 RModularityOptimizer.cpp:9: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 RModularityOptimizer.cpp:9: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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; | ^ RModularityOptimizer.cpp:165:7: warning: misleading indentation; statement is not part of the previous 'else' [-Wmisleading-indentation] 165 | Rprintf("Number of communities: %d\n", clustering->getNClusters()); | ^ RModularityOptimizer.cpp:163:5: note: previous statement is here 163 | else | ^ 6 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c data_manipulation.cpp -o data_manipulation.o In file included from data_manipulation.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 data_manipulation.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 data_manipulation.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 data_manipulation.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c fast_NN_dist.cpp -o fast_NN_dist.o clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c integration.cpp -o integration.o In file included from integration.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 integration.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 integration.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 integration.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c snn.cpp -o snn.o In file included from snn.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 snn.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 snn.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/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 snn.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c stats.cpp -o stats.o clang-19 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c valid_pointer.c -o valid_pointer.o clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Seurat.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o fast_NN_dist.o integration.o snn.o stats.o valid_pointer.o -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN_pretest/Seurat.Rcheck/00LOCK-Seurat/00new/Seurat/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Seurat)