Package: RBGL

Version: 1.13.1

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check RBGL_1.13.1.tar.gz

RetCode: 0

Time: 376.7 seconds

Status: OK

CheckDir: RBGL.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/RBGL.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-04-17 r41210)
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.13.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RBGL' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating RBGL-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating RBGL-manual.tex ... OK
* checking RBGL-manual.tex ... OK

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c bbc.cpp -o bbc.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c cliques.cpp -o cliques.o
cliques.cpp: In function `void print_one_clique(oneCliqueType&)':
cliques.cpp:110: warning: comparison between signed and unsigned integer 
   expressions
cliques.cpp: In function `void print_all_cliques(allCliquesType&, char*)':
cliques.cpp:118: warning: comparison between signed and unsigned integer 
   expressions
cliques.cpp: In function `void extend_v2(Graph_ud&, std::vector<int, 
   std::allocator<int> >&, std::vector<int, std::allocator<int> >&, int, int, 
   int&, allCliquesType&)':
cliques.cpp:138: warning: `int fixp' might be used uninitialized in this 
   function
cliques.cpp:139: warning: `int pos' might be used uninitialized in this 
   function
cliques.cpp:139: warning: `int s' might be used uninitialized in this function
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c clusteringCoef.cpp -o clusteringCoef.o
clusteringCoef.cpp: In function `int findIndex(int, const std::vector<int, 
   std::allocator<int> >&)':
clusteringCoef.cpp:132: warning: comparison between signed and unsigned integer 
   expressions
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c hcs.cpp -o hcs.o
hcs.cpp: In function `void output_graph_labels(const V_Label&, const char*)':
hcs.cpp:27: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function `void build_subgraph(Cluster&, const Graph_ud&, const 
   V_Label&, Graph_ud&, V_Label&)':
hcs.cpp:62: warning: comparison between signed and unsigned integer expressions
hcs.cpp: In function `void remove_vertices(int, const Graph_ud&, const 
   V_Label&, Graph_ud&, V_Label&)':
hcs.cpp:117: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp: In function `dst cluster_distance(const Graph_ud&, V_Label&, int, 
   V_Label&)':
hcs.cpp:134: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp:138: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp: In function `void adopt_singleton(const Graph_ud&, V_Label&, 
   ClusterResult&)':
hcs.cpp:206: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp: In function `void remove_clusters(ClusterResult&, const Graph_ud&, 
   const V_Label&, Graph_ud&, V_Label&)':
hcs.cpp:248: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp: In function `void HCS_internal(const Graph_ud&, V_Label&, 
   ClusterResult&)':
hcs.cpp:288: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp: In function `SEXPREC* HCS_loop(Graph_ud&, V_Label&)':
hcs.cpp:363: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp:393: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp:397: warning: comparison between signed and unsigned integer 
   expressions
hcs.cpp:353: warning: unused variable `bool found_new_cluster'
boostIncl/boost/graph/edge_connectivity.hpp: In function `std::pair<typename 
   boost::graph_traits<G>::vertex_descriptor, typename 
   boost::graph_traits<G>::degree_size_type> 
   boost::detail::min_degree_vertex(Graph&) [with Graph = const 
   R_adjacency_list<boost::undirectedS, double>]':
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: `size_t p' might be 
   used uninitialized in this function
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp: In function `SEXPREC* BGL_incr_comp_internal(SEXPREC*, 
   SEXPREC*, SEXPREC*, E_IC_METHOD)':
incrConnComp.cpp:67: warning: comparison between signed and unsigned integer 
   expressions
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c interfaces.cpp -o interfaces.o
interfaces.cpp: In function `SEXPREC* BGL_articulation_points_U(SEXPREC*, 
   SEXPREC*, SEXPREC*, SEXPREC*)':
interfaces.cpp:310: warning: comparison between signed and unsigned integer 
   expressions
boostIncl/boost/graph/edge_connectivity.hpp: In function `std::pair<typename 
   boost::graph_traits<G>::vertex_descriptor, typename 
   boost::graph_traits<G>::degree_size_type> 
   boost::detail::min_degree_vertex(Graph&) [with Graph = 
   R_adjacency_list<boost::undirectedS, double>]':
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: `size_t p' might be 
   used uninitialized in this function
interfaces.cpp: In function `SEXPREC* BGL_astar_search_D(SEXPREC*, SEXPREC*, 
   SEXPREC*)':
interfaces.cpp:404: warning: `SEXPREC*ansList' might be used uninitialized in 
   this function
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c layout.cpp -o layout.o
layout.cpp: In function `SEXPREC* BGL_gursov_atun_layout(SEXPREC*, SEXPREC*, 
   SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
layout.cpp:219: warning: unused variable `double w'
layout.cpp:220: warning: unused variable `double h'
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c mincut.cpp -o mincut.o
boostIncl/boost/graph/edge_connectivity.hpp: In function `std::pair<typename 
   boost::graph_traits<G>::vertex_descriptor, typename 
   boost::graph_traits<G>::degree_size_type> 
   boost::detail::min_degree_vertex(Graph&) [with Graph = 
   R_adjacency_list<boost::undirectedS, double>]':
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: `size_t p' might be 
   used uninitialized in this function
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c minST.cpp -o minST.o
minST.cpp: In function `SEXPREC* BGL_PRIM_U(SEXPREC*, SEXPREC*, SEXPREC*, 
   SEXPREC*)':
minST.cpp:99: warning: comparison between signed and unsigned integer 
   expressions
minST.cpp:103: warning: comparison between signed and unsigned integer 
   expressions
minST.cpp:93: warning: unused variable `SEXPREC*vlist'
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c ordering.cpp -o ordering.o
ordering.cpp: In function `SEXPREC* BGL_king_ordering(SEXPREC*, SEXPREC*, 
   SEXPREC*, SEXPREC*)':
ordering.cpp:172: warning: unused variable `int delta'
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp: In function `SEXPREC* 
   BGL_bellman_ford_shortest_paths(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, 
   SEXPREC*)':
shortestPath.cpp:79: warning: unused variable `int j'
shortestPath.cpp: In function `SEXPREC* 
   BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXPREC*, SEXPREC*, SEXPREC*, 
   SEXPREC*)':
shortestPath.cpp:180: warning: unused variable `const int V'
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c sna.cpp -o sna.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c transitive_closure.cpp -o transitive_closure.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -Wall -c wavefront.cpp -o wavefront.o
g++ -shared -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o hcs.o incrConnComp.o interfaces.o layout.o mincut.o minST.o ordering.o shortestPath.o sna.o transitive_closure.o wavefront.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** save image
Loading required package: graph
** help
 >>> Building/Updating help pages for package 'RBGL'
     Formats: text html latex example 
  FileDep                           text    html    latex   example
  RBGL.overview                     text    html    latex
  astarSearch                       text    html    latex   example
  bandwidth                         text    html    latex   example
  bccluster                         text    html    latex   example
  bellman.ford.sp                   text    html    latex   example
  betweenness                       text    html    latex   example
  bfs                               text    html    latex   example
  biConnComp                        text    html    latex   example
  clusteringCoef                    text    html    latex   example
  clusteringCoefAppr                text    html    latex   example
  coloring                          text    html    latex   example
  connectedComp                     text    html    latex   example
  dag.sp                            text    html    latex   example
  dijkstra.sp                       text    html    latex   example
  edgeConn                          text    html    latex   example
  extractPath                       text    html    latex   example
  floyd.warshall.all.pairs.sp       text    html    latex   example
  gprofile                          text    html    latex   example
  graphGenerator                    text    html    latex   example
  highlyConnSG                      text    html    latex   example
  incrConnComp                      text    html    latex   example
  is.triangulated                   text    html    latex   example
  isomorphism                       text    html    latex   example
  johnson.all.pairs.sp              text    html    latex   example
  kCliques                          text    html    latex   example
  kCores                            text    html    latex   example
  lambdaSets                        text    html    latex   example
  layout                            text    html    latex   example
  maxClique                         text    html    latex   example
  maxFlow                           text    html    latex   example
  minCut                            text    html    latex   example
  mstree.kruskal                    text    html    latex   example
  mstree.prim                       text    html    latex   example
  ordering                          text    html    latex   example
  removeSelfLoops                   text    html    latex   example
  separates                         text    html    latex   example
  sp.between                        text    html    latex   example
  strongComp                        text    html    latex   example
  transClosure                      text    html    latex   example
  transitivity                      text    html    latex   example
  tsort                             text    html    latex   example
  wavefront                         text    html    latex   example
** building package indices ...
* DONE (RBGL)