############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rtreemix ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘Rtreemix’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rtreemix.cc -o Rtreemix.o In file included from include/replaceleda.hh:7, from include/max_weight_branch.h:25, from include/mtree.h:14, from include/mtreemix.h:14, from Rtreemix.cc:3: Rtreemix.cc: In function ‘SEXPREC* R_fit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ Rtreemix.cc:596:7: note: in expansion of macro ‘forall_nodes’ 596 | forall_nodes (n, G[k]) { | ^~~~~~~~~~~~ Rtreemix.cc: In function ‘SEXPREC* R_fit1(SEXP, SEXP, SEXP, SEXP)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ Rtreemix.cc:938:7: note: in expansion of macro ‘forall_nodes’ 938 | forall_nodes (n, G[k]) { | ^~~~~~~~~~~~ Rtreemix.cc: In function ‘SEXPREC* R_fit0(SEXP, SEXP, SEXP, SEXP)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ Rtreemix.cc:1281:7: note: in expansion of macro ‘forall_nodes’ 1281 | forall_nodes (n, G[k]) { | ^~~~~~~~~~~~ Rtreemix.cc: In function ‘SEXPREC* R_bootstrap(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ Rtreemix.cc:1728:7: note: in expansion of macro ‘forall_nodes’ 1728 | forall_nodes (n, G[k]) { | ^~~~~~~~~~~~ Rtreemix.cc: In function ‘SEXPREC* R_random(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ Rtreemix.cc:2629:7: note: in expansion of macro ‘forall_nodes’ 2629 | forall_nodes (n, G[k]) { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rtreemix_patch.cc -o Rtreemix_patch.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c WrapGraph.cc -o WrapGraph.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cfunctions.cc -o cfunctions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c kmeans.cc -o kmeans.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c max_weight_branch.cc -o max_weight_branch.o In file included from include/replaceleda.hh:7, from include/max_weight_branch.h:25, from max_weight_branch.cc:11: max_weight_branch.cc: In function ‘void DOT(replaceleda::graph&, replaceleda::map, std::__cxx11::basic_string >&, replaceleda::map, double>&, char*)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ max_weight_branch.cc:97:3: note: in expansion of macro ‘forall_nodes’ 97 | forall_nodes(v, G) | ^~~~~~~~~~~~ max_weight_branch.cc: In function ‘replaceleda::list > max_weight_subgraph_indeg_le_1(replaceleda::graph&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ max_weight_branch.cc:142:3: note: in expansion of macro ‘forall_nodes’ 142 | forall_nodes(v, G) // choose heaviest inedge | ^~~~~~~~~~~~ max_weight_branch.cc: In function ‘void contract_all_cycles(replaceleda::graph&, int, replaceleda::array > >, replaceleda::GRAPH, replaceleda::RefCountPtr >&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ max_weight_branch.cc:341:3: note: in expansion of macro ‘forall_nodes’ 341 | forall_nodes(v, G) | ^~~~~~~~~~~~ max_weight_branch.cc: In function ‘replaceleda::list > MAX_WEIGHT_BRANCHING(replaceleda::graph&, replaceleda::map, std::__cxx11::basic_string >&, replaceleda::edge_array&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ max_weight_branch.cc:432:3: note: in expansion of macro ‘forall_nodes’ 432 | forall_nodes(v, G[0]) // node labels | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mtree.cc -o mtree.o In file included from include/replaceleda.hh:7, from include/max_weight_branch.h:25, from include/mtree.h:14, from mtree.cc:12: mtree.cc: In function ‘void mgraph_init(replaceleda::array >&, replaceleda::graph&, replaceleda::map, std::__cxx11::basic_string >&, replaceleda::edge_array&, replaceleda::map >&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mtree.cc:185:3: note: in expansion of macro ‘forall_nodes’ 185 | forall_nodes(v, G) | ^~~~~~~~~~~~ include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mtree.cc:186:5: note: in expansion of macro ‘forall_nodes’ 186 | forall_nodes(w, G) | ^~~~~~~~~~~~ mtree.cc: In function ‘replaceleda::list > mtree_bfs(replaceleda::graph&, replaceleda::node&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mtree.cc:272:3: note: in expansion of macro ‘forall_nodes’ 272 | forall_nodes(w, G) | ^~~~~~~~~~~~ mtree.cc: In function ‘double mtree_like(replaceleda::integer_vector&, replaceleda::graph&, replaceleda::map >&, replaceleda::map, double>&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mtree.cc:321:3: note: in expansion of macro ‘forall_nodes’ 321 | forall_nodes(w, G) | ^~~~~~~~~~~~ mtree.cc: In function ‘replaceleda::integer_vector mtree_draw(int, replaceleda::graph&, replaceleda::node&, replaceleda::map, double>&, replaceleda::map, int>&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mtree.cc:444:3: note: in expansion of macro ‘forall_nodes’ 444 | forall_nodes(w, G) | ^~~~~~~~~~~~ mtree.cc: In function ‘void mtree_directed(replaceleda::graph&, replaceleda::node&, replaceleda::map, double>&, double, double)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mtree.cc:784:3: note: in expansion of macro ‘forall_nodes’ 784 | forall_nodes(w, G) | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mtreemix.cc -o mtreemix.o In file included from include/replaceleda.hh:7, from include/max_weight_branch.h:25, from include/mtree.h:14, from mtreemix.cc:11: mtreemix.cc: In function ‘double mtree_state(replaceleda::map, int>&, replaceleda::integer_vector&, replaceleda::graph&, replaceleda::map >&, replaceleda::map, double>&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mtreemix.cc:1035:3: note: in expansion of macro ‘forall_nodes’ 1035 | forall_nodes(w, G) | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c replaceleda.cc -o replaceleda.o In file included from include/replaceleda.hh:7, from replaceleda.cc:2: replaceleda.cc: In function ‘bool replaceleda::Is_Acyclic(replaceleda::graph&, replaceleda::list >&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ replaceleda.cc:81:5: note: in expansion of macro ‘forall_nodes’ 81 | forall_nodes(v,G) | ^~~~~~~~~~~~ replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::graph&, replaceleda::graph&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ replaceleda.cc:128:5: note: in expansion of macro ‘forall_nodes’ 128 | forall_nodes(v, g_source){ | ^~~~~~~~~~~~ replaceleda.cc: In function ‘void replaceleda::CopyGraph(replaceleda::GRAPH, replaceleda::RefCountPtr >&, replaceleda::graph&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ replaceleda.cc:149:5: note: in expansion of macro ‘forall_nodes’ 149 | forall_nodes(v, g_source){ | ^~~~~~~~~~~~ replaceleda.cc: In function ‘std::ostream& replaceleda::operator<<(std::ostream&, replaceleda::graph&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ replaceleda.cc:352:5: note: in expansion of macro ‘forall_nodes’ 352 | forall_nodes(v, g){ | ^~~~~~~~~~~~ replaceleda.cc: In function ‘void replaceleda::printGraph(replaceleda::graph&, replaceleda::edge_array&)’: include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value] 16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() , n = G.getNode(icount);++icount) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ replaceleda.cc:373:5: note: in expansion of macro ‘forall_nodes’ 373 | forall_nodes(v, g){ | ^~~~~~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o Rtreemix.so Rtreemix.o Rtreemix_patch.o WrapGraph.o cfunctions.o kmeans.o max_weight_branch.o mtree.o mtreemix.o replaceleda.o -lm -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-Rtreemix/00new/Rtreemix/libs ** R ** data ** 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 (Rtreemix)