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Package 364/467HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.28.0
Li Long
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/RBGL
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: RBGL
Version: 1.28.0
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch RBGL_1.28.0.tar.gz
StartedAt: 2011-10-20 16:33:09 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 16:35:11 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 121.9 seconds
RetCode: 0
Status:  OK  
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/RBGL.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RBGL' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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 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 ... NOTE
prepare_Rd: astarSearch.Rd:14-15: Dropping empty section \value
prepare_Rd: astarSearch.Rd:27: Dropping empty section \seealso
prepare_Rd: bandwidth.Rd:36: Dropping empty section \seealso
prepare_Rd: biConnComp.Rd:52: Dropping empty section \seealso
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:16-17: Dropping empty section \details
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:19-20: Dropping empty section \value
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:33-34: Dropping empty section \examples
prepare_Rd: chrobakPayneStraightLineDrawing.Rd:16-17: Dropping empty section \details
prepare_Rd: chrobakPayneStraightLineDrawing.Rd:19-20: Dropping empty section \value
prepare_Rd: coloring.Rd:42: Dropping empty section \seealso
prepare_Rd: dominatorTree.Rd:37: Dropping empty section \seealso
prepare_Rd: edmondsMaxCardinalityMatching.Rd:16-17: Dropping empty section \details
prepare_Rd: edmondsMaxCardinalityMatching.Rd:19-20: Dropping empty section \value
prepare_Rd: edmondsOptimumBranching.Rd:20-21: Dropping empty section \value
prepare_Rd: gprofile.Rd:37: Dropping empty section \seealso
prepare_Rd: is.triangulated.Rd:43: Dropping empty section \seealso
prepare_Rd: isKuratowskiSubgraph.Rd:16-17: Dropping empty section \details
prepare_Rd: isKuratowskiSubgraph.Rd:19-20: Dropping empty section \value
prepare_Rd: isStraightLineDrawing.Rd:17-18: Dropping empty section \details
prepare_Rd: isStraightLineDrawing.Rd:20-21: Dropping empty section \value
prepare_Rd: isomorphism.Rd:42: Dropping empty section \seealso
prepare_Rd: johnson.all.pairs.sp.Rd:34: Dropping empty section \note
prepare_Rd: kCliques.Rd:45: Dropping empty section \seealso
prepare_Rd: kCores.Rd:39: Dropping empty section \seealso
prepare_Rd: lambdaSets.Rd:45: Dropping empty section \seealso
prepare_Rd: makeBiconnectedPlanar.Rd:16-17: Dropping empty section \details
prepare_Rd: makeBiconnectedPlanar.Rd:19-20: Dropping empty section \value
prepare_Rd: makeConnected.Rd:16-17: Dropping empty section \details
prepare_Rd: makeConnected.Rd:19-20: Dropping empty section \value
prepare_Rd: makeMaximalPlanar.Rd:16-17: Dropping empty section \details
prepare_Rd: makeMaximalPlanar.Rd:19-20: Dropping empty section \value
prepare_Rd: maxClique.Rd:35: Dropping empty section \seealso
prepare_Rd: maximumCycleRatio.Rd:16-17: Dropping empty section \details
prepare_Rd: maximumCycleRatio.Rd:19-20: Dropping empty section \value
prepare_Rd: maximumCycleRatio.Rd:33-34: Dropping empty section \examples
prepare_Rd: minimumCycleRatio.Rd:16-17: Dropping empty section \details
prepare_Rd: minimumCycleRatio.Rd:19-20: Dropping empty section \value
prepare_Rd: minimumCycleRatio.Rd:33-34: Dropping empty section \examples
prepare_Rd: ordering.Rd:77: Dropping empty section \seealso
prepare_Rd: planarCanonicalOrdering.Rd:16-17: Dropping empty section \details
prepare_Rd: planarCanonicalOrdering.Rd:19-20: Dropping empty section \value
prepare_Rd: planarFaceTraversal.Rd:16-17: Dropping empty section \details
prepare_Rd: planarFaceTraversal.Rd:19-20: Dropping empty section \value
prepare_Rd: removeSelfLoops.Rd:27: Dropping empty section \seealso
prepare_Rd: sloanStartEndVertices.Rd:16-17: Dropping empty section \details
prepare_Rd: sloanStartEndVertices.Rd:19-20: Dropping empty section \value
prepare_Rd: sloanStartEndVertices.Rd:33-34: Dropping empty section \examples
prepare_Rd: transClosure.Rd:36: Dropping empty section \seealso
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: XML
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

RBGL.Rcheck/00install.out:

* installing *source* package 'RBGL' ...
found boostIncl header sources and tar archive;\n using what is there.
** libs
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c bbc.cpp -o bbc.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from bbc.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c cliques.cpp -o cliques.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from cliques.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c clusteringCoef.cpp -o clusteringCoef.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from clusteringCoef.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
clusteringCoef.cpp: In function 'SEXPREC* graphGenerator(SEXPREC*, SEXPREC*, SEXPREC*)':
clusteringCoef.cpp:394:40: warning: 'u' may be used uninitialized in this function
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c dominatorTree.cpp -o dominatorTree.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from dominatorTree.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from edmonds_optimum_branching.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c hcs.cpp -o hcs.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from hcs.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c incrConnComp.cpp -o incrConnComp.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from incrConnComp.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c interfaces.cpp -o interfaces.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from interfaces.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c layout.cpp -o layout.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from layout.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
layout.cpp: In function 'SEXPREC* BGL_layout_internal(E_LAYOUT_METHOD, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
layout.cpp:116:20: warning: unused variable 'r'
layout.cpp:117:20: warning: unused variable 'w'
layout.cpp:118:20: warning: unused variable 'h'
In file included from layout.cpp:9:0:
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::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, PositionMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >*, boost::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs<double, boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >*, boost::simple_point<double>, boost::simple_point<double>&, vertex_position_t> >, Cooling = boost::linear_cooling<double>, DisplacementMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::simple_point<double>*, std::vector<boost::simple_point<double>, std::allocator<boost::simple_point<double> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, unsigned int>, boost::simple_point<double>, boost::simple_point<double>&>]':
fruchterman_reingold.hpp:423:7:   instantiated from 'static void boost::detail::fr_force_directed_layout<boost::detail::error_property_not_found>::run(const Graph&, PositionMap, Dim, Dim, AttractiveForce, RepulsiveForce, ForcePairs, Cooling, boost::detail::error_property_not_found, const boost::bgl_named_params<Param, Tag, Rest>&) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, PositionMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >*, boost::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double, AttractiveForce = boost::square_distance_attractive_force, RepulsiveForce = boost::square_distance_repulsive_force, ForcePairs = boost::grid_force_pairs<double, boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >*, boost::simple_point<double>, boost::simple_point<double>&, vertex_position_t> >, Cooling = boost::linear_cooling<double>, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
fruchterman_reingold.hpp:449:3:   instantiated from 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim, const boost::bgl_named_params<P, T, R>&) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, PositionMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >*, boost::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double, Param = boost::square_distance_attractive_force, Tag = boost::attractive_force_t, Rest = boost::no_property]'
fruchterman_reingold.hpp:470:3:   instantiated from 'void boost::fruchterman_reingold_force_directed_layout(const Graph&, PositionMap, Dim, Dim) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, PositionMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int, boost::property<vertex_position_t, boost::simple_point<double> > >, boost::property<boost::edge_weight_t, double> >*, boost::simple_point<double>, boost::simple_point<double>&, vertex_position_t>, Dim = double]'
layout.cpp:112:66:   instantiated from here
fruchterman_reingold.hpp:354:7: warning: suggest parentheses around assignment used as truth value
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c minST.cpp -o minST.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from minST.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c mincut.cpp -o mincut.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from mincut.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c ordering.cpp -o ordering.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from ordering.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c planar.cpp -o planar.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from planar.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
planar.cpp: In function 'SEXPREC* planarFaceTraversal(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:151:45: warning: comparison between signed and unsigned integer expressions
planar.cpp:153:53: warning: comparison between signed and unsigned integer expressions
planar.cpp:161:50: warning: comparison between signed and unsigned integer expressions
planar.cpp:165:58: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* planarCanonicalOrdering(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:256:40: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* isStraightLineDrawing(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:369:44: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* isKuratowskiSubgraph(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:461:6: warning: unused variable 'i'
planar.cpp: In function 'SEXPREC* makeConnected(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:485:42: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function 'SEXPREC* makeBiconnectedPlanar(SEXPREC*, SEXPREC*, SEXPREC*)':
planar.cpp:539:45: warning: comparison between signed and unsigned integer expressions
In file included from planar.cpp:6:0:
boostIncl/boost/graph/chrobak_payne_drawing.hpp: In function 'void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >, PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, unsigned int> >, ForwardIterator = __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int> >, GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<coord_t*, std::vector<coord_t> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, unsigned int>]':
boostIncl/boost/graph/chrobak_payne_drawing.hpp:208:22: warning: 'next_to_rightmost' may be used uninitialized in this function
In file included from planar.cpp:5:0:
boostIncl/boost/graph/planar_canonical_ordering.hpp: In function 'void boost::planar_canonical_ordering(const Graph&, PlanarEmbedding, OutputIterator, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >, PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, unsigned int> >, OutputIterator = std::back_insert_iterator<std::vector<unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, unsigned int>]':
boostIncl/boost/graph/planar_canonical_ordering.hpp:68:14: warning: 'second_vertex' may be used uninitialized in this function
In file included from boostIncl/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
                 from planar.cpp:3:
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function 'void boost::boyer_myrvold_impl<Graph, VertexIndexMap, StoreOldHandlesPolicy, StoreEmbeddingPolicy>::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, unsigned int> > >, EdgeIndexMap = boost::adj_list_edge_property_map<boost::undirected_tag, int, int&, unsigned int, boost::property<boost::edge_index_t, int>, boost::edge_index_t>, Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, unsigned int>, StoreOldHandlesPolicy = boost::graph::detail::store_old_handles, StoreEmbeddingPolicy = boost::graph::detail::no_embedding]':
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1279:16: warning: 'previous_vertex' may be used uninitialized in this function
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1238:16: warning: 'bicomp_root' may be used uninitialized in this function
boostIncl/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1237:16: warning: 'z' may be used uninitialized in this function
In file included from planar.cpp:11:0:
boostIncl/boost/graph/max_cardinality_matching.hpp: In member function 'bool boost::edmonds_augmenting_path_finder<Graph, MateMap, VertexIndexMap>::augment_matching() [with Graph = R_adjacency_list<boost::undirectedS, int>, MateMap = unsigned int*, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, unsigned int>]':
boostIncl/boost/graph/max_cardinality_matching.hpp:231:27: warning: 'v' may be used uninitialized in this function
boostIncl/boost/graph/max_cardinality_matching.hpp:231:29: warning: 'w' may be used uninitialized in this function
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c shortestPath.cpp -o shortestPath.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from shortestPath.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c sna.cpp -o sna.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from sna.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c transitive_closure.cpp -o transitive_closure.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from transitive_closure.cpp:16:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"       -IboostIncl    -O2 -Wall  -c wavefront.cpp -o wavefront.o
In file included from c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from wavefront.cpp:1:
c:\rtools214\mingw\bin\../lib/gcc/mingw32/4.5.0/include/c++/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -shared -s -static-libgcc -o RBGL.dll tmp.def bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o layout.o minST.o mincut.o ordering.o planar.o shortestPath.o sna.o transitive_closure.o wavefront.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/RBGL.Rcheck/RBGL/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RBGL)

RBGL.Rcheck/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.800.020.90
astarSearch0.010.000.03
bandwidth0.020.000.02
bccluster0.010.000.01
bellman.ford.sp0.010.000.02
betweenness000
bfs0.020.000.02
biConnComp0.000.010.01
chrobakPayneStraightLineDrawing0.010.000.03
clusteringCoef0.020.000.02
clusteringCoefAppr0.010.000.01
coloring0.020.000.02
connectedComp0.010.000.06
dag.sp0.020.000.02
dijkstra.sp0.050.000.05
dominatorTree000
edgeConn0.000.020.03
edmondsMaxCardinalityMatching0.030.000.03
edmondsOptimumBranching0.010.000.01
extractPath000
floyd.warshall.all.pairs.sp0.020.000.02
gprofile0.010.000.01
graphGenerator000
highlyConnSG0.020.000.02
incrConnComp0.020.000.02
is.triangulated0.010.000.01
isKuratowskiSubgraph0.020.000.01
isStraightLineDrawing0.010.000.02
isomorphism0.000.020.01
johnson.all.pairs.sp0.020.000.02
kCliques0.010.000.02
kCores0.070.000.06
lambdaSets0.030.000.03
layout0.010.000.01
makeBiconnectedPlanar0.020.000.02
makeConnected0.020.000.01
makeMaximalPlanar0.020.000.02
maxClique0.030.000.03
maxFlow0.010.000.01
minCut0.020.000.02
mstree.kruskal0.030.000.03
mstree.prim000
ordering0.040.000.03
planarCanonicalOrdering0.010.000.01
planarFaceTraversal000
removeSelfLoops0.030.000.03
separates0.020.000.02
sp.between0.050.000.05
strongComp0.010.000.01
transClosure0.030.000.05
transitivity000
tsort000
wavefront0.010.000.01