* installing *source* package ‘dodgr’ ... ** package ‘dodgr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/dodgr/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c heaps/bheap.cpp -o heaps/bheap.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c heaps/fheap.cpp -o heaps/fheap.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c heaps/heap23.cpp -o heaps/heap23.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c heaps/triheap_ext.cpp -o heaps/triheap_ext.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c heaps/triheap.cpp -o heaps/triheap.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c centrality.cpp -o centrality.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c deduplicate.cpp -o deduplicate.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c dgraph.cpp -o dgraph.o In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7, from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6, from run_sp.h:13, from centrality.cpp:1: /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]': /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:57:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = OneCentralityEdge; std::size_t = long unsigned int]' centrality.cpp:452:38: required from here /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 16 | if (requestedValue != defaultValue && requestedValue > 0) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c pathfinders.cpp -o pathfinders.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c dodgr-to-sf.cpp -o dodgr-to-sf.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c flows.cpp -o flows.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c fund-cycles.cpp -o fund-cycles.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c graph-contract.cpp -o graph-contract.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c graph.cpp -o graph.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c graph-sample.cpp -o graph-sample.o In file included from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/TinyThread.h:7, from /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:6, from run_sp.h:13, from flows.cpp:2: /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]': /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel.h:57:28: required from 'void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = OneAggregate; std::size_t = long unsigned int]' flows.cpp:598:34: required from here /data/gannet/ripley/R/test-dev/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 16 | if (requestedValue != defaultValue && requestedValue > 0) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ graph.cpp: In function 'Rcpp::List rcpp_get_component_vector(const Rcpp::DataFrame&)': graph.cpp:198:10: warning: variable 'has_times' set but not used [-Wunused-but-set-variable] 198 | bool has_times = graph::graph_from_df (graph, vertices, edge_map, vert2edge_map); | ^~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c match-points.cpp -o match-points.o graph-sample.cpp: In function 'Rcpp::StringVector rcpp_sample_graph(Rcpp::DataFrame, size_t)': graph-sample.cpp:109:10: warning: variable 'has_times' set but not used [-Wunused-but-set-variable] 109 | bool has_times = graph::graph_from_df (graph, vertices, edge_map, vert2edge_map); | ^~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c run_sp.cpp -o run_sp.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c run_sp_categorical.cpp -o run_sp_categorical.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c sc-as-network.cpp -o sc-as-network.o match-points.cpp: In member function 'virtual void OneEdgeIndex::operator()(std::size_t, std::size_t)': match-points.cpp:99:17: warning: variable 'which_side' set but not used [-Wunused-but-set-variable] 99 | int which_side = INFINITE_INT; | ^~~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c sf-as-network.cpp -o sf-as-network.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/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 -c turn_penalty.cpp -o turn_penalty.o g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o dodgr.so heaps/bheap.o heaps/fheap.o heaps/heap23.o heaps/triheap_ext.o heaps/triheap.o centrality.o deduplicate.o dgraph.o pathfinders.o dodgr-to-sf.o flows.o fund-cycles.o graph-contract.o graph.o graph-sample.o match-points.o RcppExports.o run_sp.o run_sp_categorical.o sc-as-network.o sf-as-network.o turn_penalty.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/dodgr/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/dodgr/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/dodgr/src' installing to /data/gannet/ripley/R/packages/tests-devel/dodgr.Rcheck/00LOCK-dodgr/00new/dodgr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (dodgr)