BioC 3.2: CHECK report for Rtreemix on zin1

Package: Rtreemix

Version: 1.32.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rtreemix_1.32.0.tar.gz

StartedAt: 2016-04-23 05:08:44 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:10:29 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 104.8 seconds

RetCode: 0

Status:  OK

CheckDir: Rtreemix.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rtreemix_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rtreemix.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.32.0’
* 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 ... [43s/44s] OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
* 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 ‘upRight’
.plott1: no visible global function definition for ‘boundBox’
.plott1: no visible global function definition for ‘getX’
.plott1: no visible global function definition for ‘getY’
.plott1: no visible global function definition for ‘getDefaultAttrs’
.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
  ‘labelFontsize’
.plott1: no visible global function definition for ‘AgEdge’
.plott2: no visible global function definition for ‘getDefaultAttrs’
.plott2: no visible global function definition for ‘removedEdges’
.plott2: no visible global function definition for ‘agopen’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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-3.2-bioc/meat/Rtreemix.Rcheck/00check.log’
for details.

* installing *source* package ‘Rtreemix’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c WrapGraph.cc -o WrapGraph.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cfunctions.cc -o cfunctions.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c kmeans.cc -o kmeans.o
g++ -I/home/biocbuild/bbs-3.2-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::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::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-3.2-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::basic_string<char> >&, replaceleda::graph&, replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::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-3.2-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-3.2-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-3.2-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-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/Rtreemix.Rcheck/Rtreemix/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘Rtreemix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rtreemix)

name	user	system	elapsed
L1.dist	0.002	0.000	0.002
L2.norm	0.001	0.000	0.000
Pval.dist	0.001	0.000	0.002
RtreemixData-class	0.02	0.00	0.02
RtreemixGPS-class	0.001	0.000	0.001
RtreemixModel-class	0.702	0.011	0.715
RtreemixSim-class	0.016	0.004	0.020
RtreemixStats-class	0.029	0.017	0.045
bootstrap-methods	0.001	0.000	0.001
comp.models	0.021	0.000	0.020
comp.trees	0.013	0.000	0.014
confIntGPS-methods	0.001	0.000	0.000
distribution-methods	0.027	0.003	0.031
fit-methods	0.178	0.000	0.178
generate-methods	0.004	0.000	0.004
get.tree.levels	0.003	0.000	0.003
gps-methods	0.001	0.000	0.001
hiv.data	0.006	0.000	0.006
kullback.leibler	0.001	0.000	0.001
likelihoods-methods	0.024	0.000	0.025
sim-methods	0.016	0.000	0.016
stability.sim	0.000	0.000	0.001