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###
### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rtreemix
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rtreemix' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
#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'
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]
#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'
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]
#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'
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]
#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'
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]
#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'
forall_nodes (n, G[k]) {
^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Rtreemix_patch.cc -o Rtreemix_patch.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c WrapGraph.cc -o WrapGraph.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c cfunctions.cc -o cfunctions.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c kmeans.cc -o kmeans.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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<replaceleda::RefCountPtr<replaceleda::Node>, std::__cxx11::basic_string<char> >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, char*)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(v, G)
^~~~~~~~~~~~
max_weight_branch.cc: In function 'replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > max_weight_subgraph_indeg_le_1(replaceleda::graph&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(v, G) // choose heaviest inedge
^~~~~~~~~~~~
max_weight_branch.cc: In function 'void contract_all_cycles(replaceleda::graph&, int, replaceleda::array<replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > >, replaceleda::GRAPH<replaceleda::RefCountPtr<replaceleda::Node>, replaceleda::RefCountPtr<replaceleda::Edge> >&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(v, G)
^~~~~~~~~~~~
max_weight_branch.cc: In function 'replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > MAX_WEIGHT_BRANCHING(replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::__cxx11::basic_string<char> >&, replaceleda::edge_array<double>&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(v, G[0]) // node labels
^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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<std::__cxx11::basic_string<char> >&, replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::__cxx11::basic_string<char> >&, replaceleda::edge_array<double>&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(v, G)
^~~~~~~~~~~~
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(w, G)
^~~~~~~~~~~~
mtree.cc: In function 'replaceleda::list<replaceleda::RefCountPtr<replaceleda::Edge> > mtree_bfs(replaceleda::graph&, replaceleda::node&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(w, G)
^~~~~~~~~~~~
mtree.cc: In function 'double mtree_like(replaceleda::integer_vector&, replaceleda::graph&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(w, G)
^~~~~~~~~~~~
mtree.cc: In function 'replaceleda::integer_vector mtree_draw(int, replaceleda::graph&, replaceleda::node&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, int>&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(w, G)
^~~~~~~~~~~~
mtree.cc: In function 'void mtree_directed(replaceleda::graph&, replaceleda::node&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&, double, double)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(w, G)
^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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<replaceleda::RefCountPtr<replaceleda::Edge>, int>&, replaceleda::integer_vector&, replaceleda::graph&, replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> >&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double>&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(w, G)
^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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<replaceleda::RefCountPtr<replaceleda::Edge> >&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
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]
#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'
forall_nodes(v, g_source){
^~~~~~~~~~~~
replaceleda.cc: In function 'void replaceleda::CopyGraph(replaceleda::GRAPH<replaceleda::RefCountPtr<replaceleda::Node>, replaceleda::RefCountPtr<replaceleda::Edge> >&, replaceleda::graph&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
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]
#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'
forall_nodes(v, g){
^~~~~~~~~~~~
replaceleda.cc: In function 'void replaceleda::printGraph(replaceleda::graph&, replaceleda::edge_array<double>&)':
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
#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'
forall_nodes(v, g){
^~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rtreemix.dll tmp.def Rtreemix.o Rtreemix_patch.o WrapGraph.o cfunctions.o kmeans.o max_weight_branch.o mtree.o mtreemix.o replaceleda.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rtreemix/00new/Rtreemix/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rtreemix'
finding HTML links ... done
L1.dist html
L2.norm html
Pval.dist html
RtreemixData-class html
RtreemixGPS-class html
RtreemixModel-class html
RtreemixSim-class html
RtreemixStats-class html
bootstrap-methods html
comp.models html
comp.trees html
confIntGPS-methods html
distribution-methods html
fit-methods html
generate-methods html
get.tree.levels html
gps-methods html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rtreemix/00new/Rtreemix/help/gps.html
hiv.data html
kullback.leibler html
likelihoods-methods html
sim-methods html
stability.sim html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rtreemix)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'plgem' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'tweeDEseq' is missing or broken
done
