* installing *source* package ‘conos’ ...
** this is package ‘conos’ version ‘1.5.2’
** package ‘conos’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/conos/src'
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c Rjnmf.cpp -o Rjnmf.o
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c adjustedRand.cpp -o adjustedRand.o
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c checkfunctions.cpp -o checkfunctions.o
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c cpca.cpp -o cpca.o
cpca.cpp: In function ‘Rcpp::List cpcaF(const arma::cube&, const arma::vec&, int, int, double, Rcpp::Nullable<Rcpp::Matrix<14> >, bool)’:
cpca.cpp:25:8: warning: unused variable ‘converged’ [-Wunused-variable]
25 | bool converged=false;
| ^~~~~~~~~
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c deltacut.cpp -o deltacut.o
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c edgeFilter.cpp -o edgeFilter.o
deltacut.cpp: In function ‘double normalized_entropy(arma::ivec&, int)’:
deltacut.cpp:110:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
110 | if(*i == labels.n_elem) { return(0.0); } // extreme case
| ~~~^~~~~~~~~~~~~~~~
deltacut.cpp: In function ‘Rcpp::List greedyModularityCutC(arma::imat&, arma::vec&, int, int, arma::ivec&, double, bool)’:
deltacut.cpp:267:13: warning: unused variable ‘ni’ [-Wunused-variable]
267 | int ni=r[i]=idm[r[i]]=leafid++;
| ^~
deltacut.cpp: In function ‘Rcpp::List _treeJaccard(arma::imat&, arma::imat&, arma::ivec&, arma::ivec&)’:
deltacut.cpp:312:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
312 | for(int i=0;i<merges.n_rows;i++) {
| ~^~~~~~~~~~~~~~
deltacut.cpp:336:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
336 | for(int j=0;j<mi.n_elem;j++) {
| ~^~~~~~~~~~
deltacut.cpp: In function ‘Rcpp::List treeJaccard(arma::imat&, arma::imat&, arma::ivec&, Rcpp::Nullable<arma::Mat<int>&>)’:
deltacut.cpp:355:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
355 | if(nleafs != clusters.n_cols) stop("number of leafs differs from the number of columns in the clusters matrix");
| ~~~~~~~^~~~~~~~~~~~~~~~~~
deltacut.cpp:375:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
375 | for(int i=0;i<clm.n_rows;i++) {
| ~^~~~~~~~~~~
deltacut.cpp: In function ‘std::vector<int, std::allocator<int> > get_membership_indices(int, arma::imat&, IIVM&)’:
deltacut.cpp:405:7: warning: unused variable ‘nleafs’ [-Wunused-variable]
405 | int nleafs=merges.n_rows+1; // number of leafs in the tree
| ^~~~~~
deltacut.cpp: In function ‘Rcpp::List scoreTreeConsistency(arma::imat&, arma::imat&, arma::ivec&, int)’:
deltacut.cpp:429:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
429 | for(int i=0;i<ref.n_rows;i++) {
| ~^~~~~~~~~~~
deltacut.cpp:479:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
479 | for(int i=0;i<currentCut.n_elem;i++) {
| ~^~~~~~~~~~~~~~~~~~
deltacut.cpp:484:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
484 | if(j>=leafidmap.n_elem) throw std::range_error("requesting out of range node in leafidmap");
| ~^~~~~~~~~~~~~~~~~~
deltacut.cpp:487:96: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
487 | Rcout<<"idmap violation at j="<<j<<" ("<<ni<<"); test.n_rows="<<test.n_rows<<' '<<(ni>test.n_rows)<<endl<<flush;
| ~~^~~~~~~~~~~~
deltacut.cpp:509:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
509 | for(int i=0;i<currentCut.n_elem;i++) {
| ~^~~~~~~~~~~~~~~~~~
deltacut.cpp:523:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
523 | for(int i=0;i<ref.n_rows;i++) {
| ~^~~~~~~~~~~
deltacut.cpp: In function ‘Rcpp::List maxStableClusters(arma::imat&, arma::vec&, double, int)’:
deltacut.cpp:578:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
578 | for(int i=0;i<merges.n_rows;i++) {
| ~^~~~~~~~~~~~~~
edgeFilter.cpp: In function ‘Rcpp::NumericVector pareDownHubEdges(SEXP, Rcpp::IntegerVector, int, int)’:
edgeFilter.cpp:50:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
50 | while(nedges > k && j<cido.n_elem && cid[ cido[j] ]>klow) {
| ~^~~~~~~~~~~~
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c edge_rebalancing.cpp -o edge_rebalancing.o
edge_rebalancing.cpp: In function ‘Rcpp::NumericMatrix getSumWeightMatrix(const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, bool)’:
edge_rebalancing.cpp:18:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18 | for (int i = 0; i < weights.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
edge_rebalancing.cpp: In function ‘std::vector<double> adjustWeightsByCellBalancingC(std::vector<double>, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, Rcpp::NumericMatrix)’:
edge_rebalancing.cpp:41:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
41 | for (int i = 0; i < weights.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c edgeweights.cpp -o edgeweights.o
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c gradients.cpp -o gradients.o
edgeweights.cpp: In member function ‘Eigen::SparseMatrix<double, 0, int> ReferenceEdges::getWIJ()’:
edgeweights.cpp:149:31: warning: comparison of integer expressions of different signedness: ‘edgeidxtype’ {aka ‘int’} and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
149 | for (edgeidxtype i = 0; i < edge_from.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
gradients.cpp: In member function ‘distancetype Gradient::distAndVector(const coordinatetype*, const coordinatetype*, coordinatetype*) const’:
gradients.cpp:21:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const dimidxtype’ {aka ‘const unsigned int’} [-Wsign-compare]
21 | for (int d = 0; d < D; d++) {
| ~~^~~
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c graph_embedding.cpp -o graph_embedding.o
graph_embedding.cpp: In function ‘std::unordered_map<int, double> get_hitting_time_map(const std::vector<int>&, const std::vector<double>&)’:
graph_embedding.cpp:66:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
66 | for (int v2 = 0; v2 < adjacent_ids.size(); ++v2) {
| ~~~^~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp: In function ‘void dfs_hitting_time(const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&, int, std::vector<bool>&, path_map_t&, double, int, double, int, double)’:
graph_embedding.cpp:126:55: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, Paths>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
126 | if ((current_prob < min_prob && result_paths.size() >= min_visited_verts) || current_prob < min_prob_lower)
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp:131:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
131 | for (int i = 0; i < adjacency_list.at(vertex_id).size(); ++i)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp: In function ‘std::pair<std::vector<double>, std::vector<int> > hitting_time_per_neighbor(const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&, int, double, int, double, int)’:
graph_embedding.cpp:152:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
152 | if (start_vertex < 0 || start_vertex >= adjacency_list.size())
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp: In function ‘std::pair<std::vector<std::vector<int> >, std::vector<std::vector<double> > > hitting_time_per_neighbors(const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&, int, int, double, int, double, int, bool)’:
graph_embedding.cpp:188:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
188 | if (n_verts <= 0 || n_verts >= adjacency_list.size()) {
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp: In function ‘Rcpp::List commute_time_per_node(const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&, int, int, bool)’:
graph_embedding.cpp:247:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
247 | for (int v1 = 0; v1 < adjacency_list.size(); ++v1) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp:276:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::unordered_map<int, double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
276 | for (int v1 = 0; v1 < hitting_times_map.size(); ++v1) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp: In instantiation of ‘std::vector<T> reorder(const std::vector<T>&, std::vector<long unsigned int>, size_t) [with T = double; size_t = long unsigned int]’:
graph_embedding.cpp:171:31: required from here
171 | auto values_sorted = reorder(values, sorted_ids, max_adj_num);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp:39:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
39 | for (int i = 0; i < max_size; ++i) {
| ~~^~~~~~~~~~
graph_embedding.cpp: In instantiation of ‘std::vector<T> reorder(const std::vector<T>&, std::vector<long unsigned int>, size_t) [with T = int; size_t = long unsigned int]’:
graph_embedding.cpp:172:32: required from here
172 | auto indexes_sorted = reorder(indexes, sorted_ids, max_adj_num);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp:39:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
39 | for (int i = 0; i < max_size; ++i) {
| ~~^~~~~~~~~~
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c largeVis.cpp -o largeVis.o
largeVis.cpp: In constructor ‘MomentumVisualizer::MomentumVisualizer(vertexidxtype*, vertexidxtype*, coordinatetype*, const dimidxtype&, const vertexidxtype&, const edgeidxtype&, distancetype, const iterationtype&, const float&, const unsigned int&, const double&, const double&)’:
largeVis.cpp:164:45: warning: comparison of integer expressions of different signedness: ‘vertexidxtype’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
164 | for (vertexidxtype i = 0; i != D*N; ++i) momentumarray[i] = 0;
| ~~^~~~~~
largeVis.cpp: In function ‘arma::mat sgd(arma::mat&, arma::ivec&, arma::ivec&, arma::ivec&, arma::vec&, const double&, const double&, const arma::uword&, const int&, const double&, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, const bool&, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::Vector<13> >, bool)’:
largeVis.cpp:254:43: warning: comparison of integer expressions of different signedness: ‘edgeidxtype’ {aka ‘int’} and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
254 | for (edgeidxtype e = 0; e < targets_i.n_elem; ++e) negweights[targets_i[e]]++;
| ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c propagate_labels.cpp -o propagate_labels.o
propagate_labels.cpp: In function ‘si_map_t parse_edges(const Rcpp::StringMatrix&, const std::vector<double>&, std::vector<Edge>&, s_vec_t)’:
propagate_labels.cpp:42:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
42 | if (edge_verts.nrow() != edge_weights.size() || edge_verts.ncol() != 2)
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:50:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
50 | for (size_t i = 0; i < edge_verts.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:57:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
57 | for (size_t i = 0; i < edge_verts.nrow(); ++i) { // TODO: add informative message in case vertex name is not presented in the map
| ~~^~~~~~~~~~~~~~~~~~~
propagate_labels.cpp: In function ‘Rcpp::NumericMatrix propagate_labels(const Rcpp::StringMatrix&, const std::vector<double>&, const Rcpp::StringVector&, int, bool, double, double, double, bool)’:
propagate_labels.cpp:69:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
69 | if (edge_verts.nrow() != edge_weights.size() || edge_verts.ncol() != 2)
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:80:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
80 | for (size_t i = 0; i < vert_labels.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:95:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::unordered_map<std::__cxx11::basic_string<char>, long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
95 | for (int v_id = 0; v_id < vertex_ids.size(); ++v_id) {
| ~~~~~^~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:96:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::unordered_map<std::__cxx11::basic_string<char>, long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
96 | for (int l_id = 0; l_id < label_ids.size(); ++l_id) {
| ~~~~~^~~~~~~~~~~~~~~~~~
propagate_labels.cpp: In function ‘void smooth_count_matrix_c(const std::vector<Edge>&, Mat&, int, double, double, double, bool, bool, const std::vector<bool>&)’:
propagate_labels.cpp:162:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
162 | for (size_t row_id = 0; row_id < cm_new.rows(); ++row_id) {
| ~~~~~~~^~~~~~~~~~~~~~~
propagate_labels.cpp: In function ‘SEXPREC* smooth_count_matrix(const Rcpp::StringMatrix&, const std::vector<double>&, const Rcpp::NumericMatrix&, const std::vector<bool>&, int, double, double, double, bool, bool)’:
propagate_labels.cpp:192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
192 | if (edge_verts.nrow() != edge_weights.size())
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
propagate_labels.cpp: In function ‘Rcpp::List adjacent_vertices(const Rcpp::StringMatrix&)’:
propagate_labels.cpp:228:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
228 | for (size_t i = 0; i < edge_verts.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
propagate_labels.cpp: In function ‘Rcpp::List adjacent_vertex_weights(const Rcpp::StringMatrix&, const std::vector<double>&)’:
propagate_labels.cpp:241:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
241 | for (size_t i = 0; i < edge_verts.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -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/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -I"./include" -fopenmp -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 -c spcov.cpp -o spcov.o
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o conos.so RcppExports.o Rjnmf.o adjustedRand.o checkfunctions.o cpca.o deltacut.o edgeFilter.o edge_rebalancing.o edgeweights.o gradients.o graph_embedding.o largeVis.o propagate_labels.o spcov.o -L. -lpthread -lm -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/conos/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/conos/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/conos/src'
installing to /data/gannet/ripley/R/packages/tests-devel/conos.Rcheck/00LOCK-conos/00new/conos/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for ‘getPca’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getPca’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getPca’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getOverdispersedGenes’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getOverdispersedGenes’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getOverdispersedGenes’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getOverdispersedGenes’ with signature ‘"Conos"’: no definition for class “Conos”
in method for ‘getCellNames’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getCellNames’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getCellNames’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getCellNames’ with signature ‘"Conos"’: no definition for class “Conos”
in method for ‘getGenes’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getGenes’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getGenes’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getGenes’ with signature ‘"Conos"’: no definition for class “Conos”
in method for ‘edgeMat<-’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘edgeMat<-’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘edgeMat<-’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘edgeMat’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘edgeMat’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘edgeMat’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getCountMatrix’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getCountMatrix’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getCountMatrix’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getGeneExpression’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getGeneExpression’ with signature ‘"Conos"’: no definition for class “Conos”
in method for ‘getGeneExpression’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getGeneExpression’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getRawCountMatrix’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getRawCountMatrix’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getRawCountMatrix’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getRawCountMatrix’ with signature ‘"Conos"’: no definition for class “Conos”
in method for ‘getEmbedding’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getEmbedding’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getEmbedding’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getEmbedding’ with signature ‘"Conos"’: no definition for class “Conos”
in method for ‘getClustering’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getClustering’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getClustering’ with signature ‘"Seurat"’: no definition for class “Seurat”
in method for ‘getClustering’ with signature ‘"Conos"’: no definition for class “Conos”
Note: wrong number of arguments to '*'
Note: wrong number of arguments to '*'
Note: wrong number of arguments to 'exp'
** 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 (conos)