* installing *source* package ‘Seurat’ ...
** this is package ‘Seurat’ version ‘5.2.0’
** package ‘Seurat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Seurat/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c ModularityOptimizer.cpp -o ModularityOptimizer.o
ModularityOptimizer.cpp: In constructor 'ModularityOptimizer::Network::Network(int, DVector*, std::vector<std::vector<int> >&, DVector*)':
ModularityOptimizer.cpp:204:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
204 | for (size_t j = 0; j < edge[0].size(); j++)
| ^~~
ModularityOptimizer.cpp:216:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
216 | for (; i <= nNodes; i++)
| ^~~
ModularityOptimizer.cpp: In member function 'ModularityOptimizer::Clustering ModularityOptimizer::Network::identifyComponents()':
ModularityOptimizer.cpp:387:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
387 | for (int l = firstNeighborIndex[node[k]]; l < firstNeighborIndex[node[k] + 1]; l++)
| ^~~
ModularityOptimizer.cpp:395:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
395 | k++;
| ^
ModularityOptimizer.cpp:377:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
377 | for (int i = 0; i < nNodes; i++)
| ^~~
ModularityOptimizer.cpp:399:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
399 | clustering.orderClustersByNNodes();
| ^~~~~~~~~~
ModularityOptimizer.cpp: In member function 'ModularityOptimizer::Network ModularityOptimizer::Network::createSubnetwork(const ModularityOptimizer::Clustering&, int, IVector&, IVector&, IVector&, DVector&) const':
ModularityOptimizer.cpp:429:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
429 | for (int k = firstNeighborIndex[j]; k < firstNeighborIndex[j + 1]; k++)
| ^~~
ModularityOptimizer.cpp:436:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
436 | subnetwork.firstNeighborIndex[i + 1] = subnetwork.nEdges;
| ^~~~~~~~~~
ModularityOptimizer.cpp: In member function 'int ModularityOptimizer::VOSClusteringTechnique::removeCluster(int)':
ModularityOptimizer.cpp:710:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
710 | for (int j = 0; j < clustering->nClusters; j++)
| ^~~
ModularityOptimizer.cpp:721:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
721 | if (i >= 0)
| ^~
ModularityOptimizer.cpp:723:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
723 | for (int j = 0; j < network->nNodes; j++)
| ^~~
ModularityOptimizer.cpp:726:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
726 | if (cluster == clustering->nClusters - 1)
| ^~
ModularityOptimizer.cpp: In member function 'void ModularityOptimizer::VOSClusteringTechnique::removeSmallClusters(int)':
ModularityOptimizer.cpp:740:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
740 | for (int k = 0; k < vosClusteringTechnique.clustering->nClusters; k++)
| ^~~
ModularityOptimizer.cpp:747:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
747 | if (i >= 0)
| ^~
ModularityOptimizer.cpp: In function 'std::shared_ptr<ModularityOptimizer::Network> ModularityOptimizer::matrixToNetwork(IVector&, IVector&, DVector&, int, int)':
ModularityOptimizer.cpp:764:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
764 | for (size_t i = 0; i < node1.size(); i++)
| ^~~
ModularityOptimizer.cpp:771:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
771 | IVector firstNeighborIndex(nNodes + 1);
| ^~~~~~~
ModularityOptimizer.cpp:783:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
783 | for (size_t i = 0; i < node1.size(); i++)
| ^~~
ModularityOptimizer.cpp:796:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
796 | if (modularityFunction == 1)
| ^~
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());
| ^~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RModularityOptimizer.cpp -o RModularityOptimizer.o
RModularityOptimizer.cpp: In function 'Rcpp::IntegerVector RunModularityClusteringCpp(Eigen::SparseMatrix<double, 0, int>, int, double, int, int, int, int, bool, std::string)':
RModularityOptimizer.cpp:163:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
163 | else
| ^~~~
RModularityOptimizer.cpp:165:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
165 | Rprintf("Number of communities: %d\n", clustering->getNClusters());
| ^~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c data_manipulation.cpp -o data_manipulation.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c fast_NN_dist.cpp -o fast_NN_dist.o
fast_NN_dist.cpp: In function 'Rcpp::List fast_dist(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::List)':
fast_NN_dist.cpp:37:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
37 | if (x.nrow() != ngraph_size) { return List(); }
| ~~~~~~~~~^~~~~~~~~~~~~~
fast_NN_dist.cpp:51:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare]
51 | for (size_t j=0; j<neighbors.size(); ++j) {
| ~^~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c integration.cpp -o integration.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c snn.cpp -o snn.o
integration.cpp: In function 'Eigen::SparseMatrix<double, 0, int> FindWeightsC(Rcpp::NumericVector, Eigen::MatrixXd, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, Eigen::MatrixXd, Eigen::VectorXd, double, double, bool)':
integration.cpp:29:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
29 | for(int i=0; i<anchor_cells2.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~
integration.cpp:48:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
48 | for(int j=0; j<mnn_idx.size() && k<indices.size(); ++j){
| ~^~~~~~~~~~~~~~~
integration.cpp: In function 'std::vector<double> ScoreHelper(Eigen::SparseMatrix<double, 0, int>, Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, int, bool, bool)':
integration.cpp:135:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
135 | if (k_snn_i > nonzero_order.size()) k_snn_i = nonzero_order.size();
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
integration.cpp:136:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
136 | for (int j = 0; j < nonzero_order.size(); ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
integration.cpp:139:26: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
139 | if(bw_dists.size() < k_snn_i || nonzero[nonzero_order[j]] == nonzero[nonzero_order[k_snn_i-1]]) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~
integration.cpp:148:25: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
148 | if (bw_dists.size() > k_snn_i) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~
snn.cpp: In function 'std::vector<double> SNN_SmallestNonzero_Dist(Eigen::SparseMatrix<double, 0, int>, Eigen::MatrixXd, int, std::vector<double>)':
snn.cpp:99:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
99 | if (n_i > nonzero_order.size()) n_i = nonzero_order.size();
| ~~~~^~~~~~~~~~~~~~~~~~~~~~
snn.cpp:101:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
101 | for (int j = 0; j < nonzero_order.size(); ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
snn.cpp:105:23: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
105 | if(dists.size() < n_i || nonzero[nonzero_order[j]] == nonzero[nonzero_order[n_i-1]]) {
| ~~~~~~~~~~~~~^~~~~
snn.cpp:117:22: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
117 | if (dists.size() > n_i) {
| ~~~~~~~~~~~~~^~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c stats.cpp -o stats.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c valid_pointer.c -o valid_pointer.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Seurat/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Seurat/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Seurat/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)