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Package 145/188OSArchBUILDCHECKBUILD BIN

RBGL

1.10.0

Li Long		Linux (SUSE 9.2) x86_64 OK  OK 
Linux (SUSE 9.2) i686 OK  OK 
Solaris 2.9 sparc OK [ ERROR ]
Windows Server 2003 x86_64 OK  OK  OK 
Package: RBGL
Version: 1.10.0
Command: /loc/biocbuild/1.9d/R/bin/R CMD check RBGL_1.10.0.tar.gz
RetCode: 1
Time: 439.4 seconds
Status: ERROR
CheckDir: RBGL.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/RBGL.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.10.0'
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... 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 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 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 ...Bus Error - core dumped
 ERROR
Running examples in 'RBGL-Ex.R' failed.
The error most likely occurred in:

> ### * FileDep
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: FileDep
> ### Title: FileDep: a graphNEL object representing a file dependency
> ###   dataset example in boost graph library
> ### Aliases: FileDep
> ### Keywords: graphs
> 
> ### ** Examples
> 
> # this is how the graph of data(FileDep) was obtained
> library(graph)
> fd <- file(system.file("XML/FileDep.gxl",package="RBGL"), open="r")
> show(fromGXL(fd))
Loading required package: XML

Attaching package: 'XML'


	The following object(s) are masked from package:graph :

	 addNode 

A graphNEL graph with directed edges
Number of Nodes = 15 
Number of Edges = 19 
> if (require(Rgraphviz))
+  {
+  data(FileDep)
+  plot(FileDep)
+  }
Loading required package: Rgraphviz
Loading required package: geneplotter
Loading required package: annotate
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

KernSmooth 2.22 installed
Copyright M. P. Wand 1997

 *** caught bus error ***
address 1f4b28c, cause 'invalid alignment'

Traceback:
 1: .Call("Rgraphviz_buildEdgeList", aa, edgemode(graph), subGList,     edgeNames, removed, edgeAttrs, defAttrs, PACKAGE = "Rgraphviz")
 2: buildEdgeList(graph, recipEdges, edgeAttrs, subGList, attrs$edge)
 3: agopen(x, name = name, layout = TRUE, layoutType = y, attrs = attrs,     nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs, subGList = subGList,     recipEdges = recipEdges)
 4: .local(x, y, ...)
 5: plot(FileDep)
 6: plot(FileDep)
aborting ...

RBGL.Rcheck/00install.out:

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c bbc.cpp -o bbc.o
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'void boost::detail::dijkstra_dispatch2(const VertexListGraph&, typename boost::graph_traits::vertex_descriptor, DistanceMap, WeightMap, IndexMap, const Params&, ColorMap) [with VertexListGraph = boost::adjacency_list >, boost::property >, boost::no_property, boost::listS>, DistanceMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator > >, boost::vec_adj_list_vertex_id_map >, unsigned int>, double, double&>, WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>, IndexMap = boost::vec_adj_list_vertex_id_map >, unsigned int>, Params = boost::bgl_named_params >, boost::property >, boost::no_property, boost::listS>, boost::adj_list_edge_property_map >, boost::edge_weight_t>, boost::iterator_property_map<__gnu_cxx::__normal_iterator, std::allocator > >*, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >, boost::vec_adj_list_vertex_id_map >, unsigned int>, std::vector, std::allocator > >, std::vector, std::allocator > >&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator > >, boost::vec_adj_list_vertex_id_map >, unsigned int>, double, double&>, boost::iterator_property_map<__gnu_cxx::__normal_iterator > >, boost::vec_adj_list_vertex_id_map >, unsigned int>, unsigned int, unsigned int&> >, boost::graph_visitor_t, boost::bgl_named_params > >, boost::vec_adj_list_vertex_id_map >, unsigned int>, double, double&>, boost::vertex_distance_t, boost::bgl_named_params >, unsigned int>, boost::vertex_index_t, boost::bgl_named_params >, boost::edge_weight_t>, boost::edge_weight_t, boost::no_property> > > >, ColorMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator > >, boost::vec_adj_list_vertex_id_map >, unsigned int>, boost::default_color_type, boost::default_color_type&>]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c cliques.cpp -o cliques.o
cliques.cpp: In function 'void print_one_clique(oneCliqueType&)':
cliques.cpp:110: warning: comparison between signed and unsigned integer expressions
cliques.cpp: In function 'void print_all_cliques(allCliquesType&, char*)':
cliques.cpp:118: warning: comparison between signed and unsigned integer expressions
cliques.cpp: In function 'void extend_v2(Graph_ud&, std::vector >&, std::vector >&, int, int, int&, allCliquesType&)':
cliques.cpp:139: warning: 's' may be used uninitialized in this function
cliques.cpp:139: warning: 'pos' may be used uninitialized in this function
cliques.cpp:138: warning: 'fixp' may be used uninitialized in this function
cliques.cpp: At global scope:
cliques.cpp:115: warning: 'void print_all_cliques(allCliquesType&, char*)' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c clusteringCoef.cpp -o clusteringCoef.o
clusteringCoef.cpp: In function 'int findIndex(int, const std::vector >&)':
clusteringCoef.cpp:132: warning: comparison between signed and unsigned integer expressions
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h: In function 'SEXPREC* graphGenerator(SEXPREC*, SEXPREC*, SEXPREC*)':
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h:104: warning: 'p$m_value' is used uninitialized in this function
clusteringCoef.cpp:394: warning: 'w' may be used uninitialized in this function
clusteringCoef.cpp: In function 'SEXPREC* clusteringCoefAppr(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
clusteringCoef.cpp:248: warning: 'w' may be used uninitialized in this function
clusteringCoef.cpp:248: warning: 'u' may be used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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 'found_new_cluster'
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h: In function 'void build_subgraph(Cluster&, const Graph_ud&, const V_Label&, Graph_ud&, V_Label&)':
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h:104: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list, OutputIterator = std::back_insert_iterator > >]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D93415$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D93415$D93380$m_value$D91177$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D93415$D93380$m_value$D91177$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D93415$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D93415$D93380$m_value$D91177$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D93415$D93380$m_value$D91177$m_source' is used uninitialized in this function
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function
hcs.cpp: At global scope:
hcs.cpp:24: warning: 'void output_graph_labels(const V_Label&, const char*)' defined but not used
hcs.cpp:32: warning: 'void output_graph(const Graph_ud&, const char*)' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)':
incrConnComp.cpp:67: warning: comparison between signed and unsigned integer expressions
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c interfaces.cpp -o interfaces.o
interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
interfaces.cpp:310: warning: comparison between signed and unsigned integer expressions
interfaces.cpp: In function 'SEXPREC* BGL_astar_search_D(SEXPREC*, SEXPREC*, SEXPREC*)':
interfaces.cpp:405: warning: 'ansList' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = Graph_ud, OutputIterator = std::back_insert_iterator, std::allocator > > >]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97943$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97943$D97908$m_value$D77866$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97943$D97908$m_value$D77866$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97943$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97943$D97908$m_value$D77866$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97943$D97908$m_value$D77866$m_source' is used uninitialized in this function
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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 'w'
layout.cpp:220: warning: unused variable 'h'
boostIncl/boost/graph/fruchterman_reingold.hpp: In function 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim, AttractiveForce, RepulsiveForce, ForcePairs, Cooling, DisplacementMap) [with Graph = boost::adjacency_list, boost::no_property> >, boost::property, boost::no_property, boost::listS>, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, boost::simple_point, boost::simple_point&>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs*, std::vector, std::allocator > > >, boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, boost::simple_point, boost::simple_point&> >, Cooling = boost::linear_cooling, DisplacementMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, boost::simple_point, boost::simple_point&>]':
boostIncl/boost/graph/fruchterman_reingold.hpp:366:   instantiated from 'static void boost::detail::fr_force_directed_layout::run(const Graph&, PositionMap, Dim, Dim, AttractiveForce, RepulsiveForce, ForcePairs, Cooling, boost::detail::error_property_not_found, const boost::bgl_named_params&) [with Graph = boost::adjacency_list, boost::no_property> >, boost::property, boost::no_property, boost::listS>, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, boost::simple_point, boost::simple_point&>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs*, std::vector, std::allocator > > >, boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, boost::simple_point, boost::simple_point&> >, Cooling = boost::linear_cooling, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
boostIncl/boost/graph/fruchterman_reingold.hpp:392:   instantiated from 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim, const boost::bgl_named_params&) [with Graph = boost::adjacency_list, boost::no_property> >, boost::property, boost::no_property, boost::listS>, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, boost::simple_point, boost::simple_point&>, Dim = double, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
boostIncl/boost/graph/fruchterman_reingold.hpp:413:   instantiated from 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim) [with Graph = IndexGraph, PositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, boost::simple_point, boost::simple_point&>, Dim = double]'
layout.cpp:187:   instantiated from here
boostIncl/boost/graph/fruchterman_reingold.hpp:312: warning: suggest parentheses around assignment used as truth value
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h: In function 'SEXPREC* BGL_gursov_atun_layout(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h:104: warning: 'p$m_value' is used uninitialized in this function
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h: In function 'SEXPREC* BGL_FRFD_layout(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h:104: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, boost::vec_adj_list_impl&) [with Graph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>, Config = boost::detail::adj_list_gen, boost::property >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property, boost::property >, boost::no_property, boost::listS>::config, Base = boost::directed_graph_helper, boost::property >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property, boost::property >, boost::no_property, boost::listS>::config>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D103864$m_value' is used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, DistanceZero) [with VertexAndEdgeListGraph = const boost::adjacency_list, boost::no_property> >, boost::property, boost::no_property, boost::listS>, DistanceMatrix = __gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, VertexID = boost::vec_adj_list_vertex_id_map, boost::no_property> >, unsigned int>, Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>, DistanceZero = double]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h: In function 'SEXPREC* BGL_layout_internal(E_LAYOUT_METHOD, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h:104: warning: 'p$m_value' is used uninitialized in this function
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h: In function 'SEXPREC* BGL_random_layout(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/../../../../include/c++/4.1.1/ext/new_allocator.h:104: warning: 'p$m_value' is used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c minST.cpp -o minST.o
minST.cpp: In function 'SEXPREC* BGL_PRIM_U(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
minST.cpp:99: warning: comparison between signed and unsigned integer expressions
minST.cpp:103: warning: comparison between signed and unsigned integer expressions
minST.cpp:93: warning: unused variable 'vlist'
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c mincut.cpp -o mincut.o
boostIncl/boost/graph/push_relabel_max_flow.hpp: In member function 'void boost::detail::push_relabel::discharge(typename boost::graph_traits::vertex_descriptor) [with Graph = boost::adjacency_list, boost::no_property> > >, boost::no_property, boost::listS>, EdgeCapacityMap = boost::adj_list_edge_property_map, boost::no_property> > >, boost::edge_capacity_t>, ResidualCapacityEdgeMap = boost::adj_list_edge_property_map, boost::no_property> > >, boost::edge_residual_capacity_t>, ReverseEdgeMap = boost::adj_list_edge_property_map, const boost::detail::edge_desc_impl&, unsigned int, const boost::property, boost::no_property> > >, boost::edge_reverse_t>, VertexIndexMap = boost::vec_adj_list_vertex_id_map, FlowValue = double]':
boostIncl/boost/graph/push_relabel_max_flow.hpp:340: warning: 'min_edge_iter$m_src' may be used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'SEXPREC* BGL_max_flow_internal(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, E_MF_METHOD)':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D76910$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D76910$D76875$m_value$D74506$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D76910$D76875$m_value$D74506$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D76910$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D76910$D76875$m_value$D74506$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D76910$D76875$m_value$D74506$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = Graph_ud, OutputIterator = std::back_insert_iterator > >]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D91054$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D91054$D91019$m_value$D74506$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D91054$D91019$m_value$D74506$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D91054$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D91054$D91019$m_value$D74506$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D91054$D91019$m_value$D74506$m_source' is used uninitialized in this function
boostIncl/boost/graph/edge_connectivity.hpp:32: warning: 'p' may be used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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 'delta'
boostIncl/boost/graph/detail/adjacency_list.hpp: In member function 'void boost::detail::mmd_impl::eliminate(typename boost::graph_traits::vertex_descriptor) [with Graph = R_adjacency_list, DegreeMap = boost::iterator_property_map, unsigned int>, int, int&>, InversePermutationMap = int*, PermutationMap = int*, SuperNodeMap = boost::iterator_property_map, unsigned int>, int, int&>, VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c shortestPath.cpp -o shortestPath.o
shortestPath.cpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
shortestPath.cpp:79: warning: unused variable 'j'
shortestPath.cpp: In function 'SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
shortestPath.cpp:180: warning: unused variable 'V'
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list, DistanceMatrix = Basic2DMatrix, VertexID = boost::vec_adj_list_vertex_id_map, unsigned int>, Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>, DistanceZero = double]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97065$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D97065$m_value' is used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c sna.cpp -o sna.o
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, boost::vec_adj_list_impl&) [with Graph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>, Config = boost::detail::adj_list_gen, boost::property >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property, boost::property >, boost::no_property, boost::listS>::config, Base = boost::directed_graph_helper, boost::property >, boost::no_property, boost::listS>, boost::vecS, boost::vecS, boost::directedS, boost::property, boost::property >, boost::no_property, boost::listS>::config>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D98157$m_value' is used uninitialized in this function
boostIncl/boost/graph/dijkstra_shortest_paths.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list, DistanceMatrix = Basic2DMatrix, VertexID = boost::vec_adj_list_vertex_id_map, unsigned int>, Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>, DistanceZero = double]':
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:80: warning: 'bfs_vis$m_decreased' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'SEXPREC* lambdaSets(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D84790$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D84790$D84755$m_value$D83094$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D84790$D84755$m_value$D83094$m_source' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D84790$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D84790$D84755$m_value$D83094$m_target' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$D84790$D84755$m_value$D83094$m_source' is used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c transitive_closure.cpp -o transitive_closure.o
boostIncl/boost/graph/detail/adjacency_list.hpp: In function 'void boost::transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap) [with Graph = R_adjacency_list, GraphTC = R_adjacency_list, G_to_TC_VertexMap = boost::iterator_property_map, unsigned int>, unsigned int, unsigned int&>, VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
boostIncl/boost/graph/detail/adjacency_list.hpp: In member function 'void boost::EdgeMutableGraphConcept::constraints() [with G = R_adjacency_list]':
boostIncl/boost/graph/detail/adjacency_list.hpp:263: warning: 'p$m_value' is used uninitialized in this function
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include   -IboostIncl  -fPIC  -g -O2 -Wall -c wavefront.cpp -o wavefront.o
g++ -G -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o hcs.o incrConnComp.o interfaces.o layout.o minST.o mincut.o ordering.o shortestPath.o sna.o transitive_closure.o wavefront.o   
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