* installing *source* package ‘sccore’ ...
** this is package ‘sccore’ version ‘1.0.6’
** package ‘sccore’ 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/sccore/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/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -I"../inst/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 -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/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -I"../inst/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 -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:70:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
70 | 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:130:55: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, Paths>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
130 | if ((current_prob < min_prob && result_paths.size() >= min_visited_verts) || current_prob < min_prob_lower)
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
graph_embedding.cpp:135:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
135 | 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:156:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
156 | 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 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:175:31: required from here
175 | 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:176:32: required from here
176 | 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/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -I"../inst/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 -c matrix_utils.cpp -o matrix_utils.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/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I/usr/local/include -I"../inst/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 -c propagate_labels.cpp -o propagate_labels.o
matrix_utils.cpp: In function ‘arma::mat jsDist(const arma::mat&)’:
matrix_utils.cpp:18:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
18 | for(int i=0; i<(m.n_cols-1); i++) {
| ~^~~~~~~~~~~~~
matrix_utils.cpp:20:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
20 | for(int j=i+1; j<m.n_cols; j++) {
| ~^~~~~~~~~
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:79:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
79 | if (edge_verts.nrow() != edge_weights.size() || edge_verts.ncol() != 2)
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:90:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
90 | for (size_t i = 0; i < vert_labels.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:105:27: 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]
105 | for (int v_id = 0; v_id < vertex_ids.size(); ++v_id) {
| ~~~~~^~~~~~~~~~~~~~~~~~~
propagate_labels.cpp:106:29: 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]
106 | 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:172:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
172 | 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:216:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
216 | if (edge_verts.nrow() != edge_weights.size())
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
propagate_labels.cpp: In function ‘Rcpp::List adjacentVertices(const Rcpp::StringMatrix&)’:
propagate_labels.cpp:262:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
262 | 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:286:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
286 | for (size_t i = 0; i < edge_verts.nrow(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~
'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 sccore.so RcppExports.o graph_embedding.o matrix_utils.o propagate_labels.o -lpthread -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
'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/sccore/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/sccore/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/sccore/src'
installing to /data/gannet/ripley/R/packages/tests-devel/sccore.Rcheck/00LOCK-sccore/00new/sccore/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for ‘embeddingPlot’ with signature ‘"Seurat"’: no definition for class “Seurat”
Note: wrong number of arguments to '*'
** 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 (sccore)