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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rtreemix_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Rtreemix.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rtreemix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rtreemix’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rtreemix’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.8Mb
sub-directories of 1Mb or more:
libs 8.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plott1: no visible binding for global variable ‘drawAgNode’
.plott1: no visible global function definition for ‘plot.new’
.plott1: no visible global function definition for ‘par’
.plott1: no visible global function definition for ‘upRight’
.plott1: no visible global function definition for ‘boundBox’
.plott1: no visible global function definition for ‘plot.window’
.plott1: no visible global function definition for ‘getX’
.plott1: no visible global function definition for ‘getY’
.plott1: no visible global function definition for ‘box’
.plott1: no visible global function definition for ‘xy.coords’
.plott1: no visible global function definition for ‘getDefaultAttrs’
.plott1: no visible global function definition for ‘plot.xy’
.plott1: no visible global function definition for ‘title’
.plott1: no visible global function definition for ‘AgNode’
.plott1 : <anonymous>: no visible global function definition for
‘getNodeRW’
.plott1 : <anonymous>: no visible global function definition for
‘getNodeLW’
.plott1 : <anonymous>: no visible global function definition for
‘getNodeHeight’
.plott1 : <anonymous>: no visible global function definition for
‘labelText’
.plott1 : <anonymous>: no visible global function definition for
‘txtLabel’
.plott1 : <anonymous>: no visible global function definition for
‘strwidth’
.plott1 : <anonymous>: no visible global function definition for
‘strheight’
.plott1 : <anonymous>: no visible global function definition for
‘labelFontsize’
.plott1: no visible global function definition for ‘AgEdge’
.plott1: no visible binding for global variable ‘lines’
.plott2: no visible global function definition for ‘getDefaultAttrs’
.plott2: no visible global function definition for ‘removedEdges’
.plott2: no visible global function definition for ‘agopen’
plot,RtreemixModel-missing: no visible global function definition for
‘par’
Undefined global functions or variables:
AgEdge AgNode agopen boundBox box drawAgNode getDefaultAttrs
getNodeHeight getNodeLW getNodeRW getX getY labelFontsize labelText
lines par plot.new plot.window plot.xy removedEdges strheight
strwidth title txtLabel upRight xy.coords
Consider adding
importFrom("grDevices", "xy.coords")
importFrom("graphics", "box", "lines", "par", "plot.new",
"plot.window", "plot.xy", "strheight", "strwidth", "title")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘Rtreemix/libs/Rtreemix.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Objects: ‘Rtreemix.o’, ‘cfunctions.o’, ‘kmeans.o’,
‘max_weight_branch.o’, ‘mtree.o’, ‘mtreemix.o’, ‘replaceleda.o’
Found ‘rand’, possibly from ‘rand’ (C)
Objects: ‘cfunctions.o’, ‘mtree.o’, ‘mtreemix.o’, ‘replaceleda.o’
Found ‘srand’, possibly from ‘srand’ (C)
Object: ‘Rtreemix.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.
* installing *source* package ‘Rtreemix’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-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:7:0,
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]) {
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rtreemix_patch.cc -o Rtreemix_patch.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c WrapGraph.cc -o WrapGraph.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cfunctions.cc -o cfunctions.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c kmeans.cc -o kmeans.o
g++ -I/home/biocbuild/bbs-3.5-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:7:0,
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
^
g++ -I/home/biocbuild/bbs-3.5-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:7:0,
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)
^
g++ -I/home/biocbuild/bbs-3.5-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:7:0,
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)
^
g++ -I/home/biocbuild/bbs-3.5-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:7:0,
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){
^
g++ -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/Rtreemix.Rcheck/Rtreemix/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rtreemix)
