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Package 404/516HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.30.1
Bioconductor Package Maintainer
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/RBGL
Last Changed Rev: 60128 / Revision: 61898
Last Changed Date: 2011-11-08 10:06:01 -0800 (Tue, 08 Nov 2011)
wilson2 Linux (openSUSE 11.4) / 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  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: RBGL
Version: 1.30.1
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch RBGL_1.30.1.tar.gz
StartedAt: 2012-01-09 05:02:03 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 05:04:05 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 121.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/RBGL.Rcheck'
* using R version 2.14.1 (2011-12-22)
* 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 '1.30.1'
* 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 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 ... NOTE
File 'RBGL/R/zzz.R':
  .onLoad has wrong argument list 'pkgname, libname'

Package startup functions should have two arguments with names starting
  with 'lib' and 'pkg', respectively.
See section 'Good practice' in ?.onAttach.

* 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 compiled code ... NOTE
File 'E:/biocbld/bbs-2.9-bioc/meat/RBGL.Rcheck/RBGL/libs/i386/RBGL.dll':
  Found '_assert', possibly from 'assert' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/include"       -IboostIncl    -O2 -Wall  -mtune=core2 -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˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/RBGL.Rcheck/RBGL/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'RBGL.Rnw' 
** testing if installed package can be loaded

* DONE (RBGL)

RBGL.Rcheck/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.660.000.80
astarSearch0.010.000.02
bandwidth0.020.000.03
bccluster0.010.000.01
bellman.ford.sp0.020.000.02
betweenness0.010.000.01
bfs0.020.000.04
biConnComp000
chrobakPayneStraightLineDrawing000
clusteringCoef0.020.000.02
clusteringCoefAppr0.000.010.01
coloring0.020.000.02
connectedComp0.010.000.04
dag.sp0.020.000.02
dijkstra.sp0.010.020.03
dominatorTree0.000.010.02
edgeConn0.020.000.01
edmondsMaxCardinalityMatching0.010.000.02
edmondsOptimumBranching000
extractPath0.020.000.01
floyd.warshall.all.pairs.sp000
gprofile0.000.020.02
graphGenerator000
highlyConnSG0.020.000.02
incrConnComp000
is.triangulated0.030.000.03
isKuratowskiSubgraph0.010.000.01
isStraightLineDrawing000
isomorphism0.020.000.02
johnson.all.pairs.sp000
kCliques0.020.000.02
kCores0.050.000.05
lambdaSets0.010.000.01
layout0.020.000.02
makeBiconnectedPlanar0.010.000.01
makeConnected0.020.000.02
makeMaximalPlanar0.010.000.01
maxClique0.020.000.02
maxFlow0.020.000.02
minCut0.010.000.01
mstree.kruskal0.030.000.03
mstree.prim0.020.000.02
ordering0.010.000.01
planarCanonicalOrdering0.020.000.02
planarFaceTraversal0.010.000.01
removeSelfLoops0.040.000.04
separates0.010.000.01
sp.between0.030.000.03
strongComp0.020.000.02
transClosure0.090.000.09
transitivity000
tsort0.000.010.02
wavefront0.020.000.01