Package: RBGL

Version: 1.32.1

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.32.1.tar.gz

StartedAt: 2012-09-24 03:10:55 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 03:13:24 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 148.8 seconds

RetCode: 0

Status:  OK

CheckDir: RBGL.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/RBGL.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.32.1’
* 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 ... NOTE
  installed size is 27.8Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the 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.

floyd.warshall.all.pairs.sp: warning in matrix(ans, nr =
  length(nodes(g))): partial argument match of 'nr' to 'nrow'
johnson.all.pairs.sp: warning in matrix(ans, nr = length(nodes(g))):
  partial argument match of 'nr' to 'nrow'
* 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 ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/RBGL.Rcheck/RBGL/libs/RBGL.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘planar.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... 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

NOTE: There were 5 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/RBGL.Rcheck/00check.log’
for details.

* installing *source* package ‘RBGL’ ...
found  rbgl_trimmed_boost_1_49_0  header sources and tar archive;\n using what is there.
** libs
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c bbc.cpp -o bbc.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c cliques.cpp -o cliques.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c clusteringCoef.cpp -o clusteringCoef.o
clusteringCoef.cpp: In function ‘SEXPREC* graphGenerator(SEXPREC*, SEXPREC*, SEXPREC*)’:
clusteringCoef.cpp:394:40: warning: ‘u’ may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c dominatorTree.cpp -o dominatorTree.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c hcs.cpp -o hcs.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -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:74:6: warning: unused variable ‘child_index’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c interfaces.cpp -o interfaces.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c minST.cpp -o minST.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c mincut.cpp -o mincut.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c ordering.cpp -o ordering.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c planar.cpp -o planar.o
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:5:0:
rbgl_trimmed_boost_1_49_0/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, long unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >, OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/planar_canonical_ordering.hpp:68:14: warning: ‘second_vertex’ may be used uninitialized in this function
In file included from rbgl_trimmed_boost_1_49_0/boost/graph/boyer_myrvold_planar_test.hpp:12:0,
                 from planar.cpp:3:
rbgl_trimmed_boost_1_49_0/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, long unsigned int> > >, EdgeIndexMap = boost::adj_list_edge_property_map<boost::undirected_tag, int, int&, long 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>, long unsigned int>, StoreOldHandlesPolicy = boost::graph::detail::store_old_handles, StoreEmbeddingPolicy = boost::graph::detail::no_embedding]’:
rbgl_trimmed_boost_1_49_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1279:16: warning: ‘previous_vertex’ may be used uninitialized in this function
rbgl_trimmed_boost_1_49_0/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1238:16: warning: ‘bicomp_root’ may be used uninitialized in this function
rbgl_trimmed_boost_1_49_0/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:6:0:
rbgl_trimmed_boost_1_49_0/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, long unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >, ForwardIterator = __gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long 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>, long unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/chrobak_payne_drawing.hpp:219:22: warning: ‘next_to_rightmost’ may be used uninitialized in this function
In file included from planar.cpp:11:0:
rbgl_trimmed_boost_1_49_0/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 = long unsigned int*, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp:231:27: warning: ‘v’ may be used uninitialized in this function
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp:231:29: warning: ‘w’ may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c shortestPath.cpp -o shortestPath.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c sna.cpp -o sna.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c transitive_closure.cpp -o transitive_closure.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c wavefront.cpp -o wavefront.o
g++ -shared -L/usr/local/lib64 -o RBGL.so bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o shortestPath.o sna.o transitive_closure.o wavefront.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/RBGL.Rcheck/RBGL/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RBGL.Rnw’ 
** testing if installed package can be loaded

* DONE (RBGL)

name	user	system	elapsed
FileDep	0.976	0.032	1.068
astarSearch	0.008	0.000	0.014
bandwidth	0.016	0.000	0.019
bccluster	0.016	0.000	0.016
bellman.ford.sp	0.016	0.000	0.020
betweenness	0.012	0.000	0.012
bfs	0.024	0.000	0.031
biConnComp	0.008	0.004	0.011
chrobakPayneStraightLineDrawing	0.016	0.000	0.016
clusteringCoef	0.020	0.000	0.024
clusteringCoefAppr	0.004	0.004	0.016
coloring	0.004	0.008	0.015
connectedComp	0.020	0.004	0.055
dag.sp	0.008	0.004	0.016
dijkstra.sp	0.032	0.000	0.035
dominatorTree	0.008	0.000	0.013
edgeConn	0.012	0.000	0.015
edmondsMaxCardinalityMatching	0.016	0.004	0.021
edmondsOptimumBranching	0.012	0.000	0.011
extractPath	0.004	0.000	0.005
floyd.warshall.all.pairs.sp	0.012	0.004	0.020
gprofile	0.004	0.004	0.013
graphGenerator	0	0	0
highlyConnSG	0.008	0.004	0.018
incrConnComp	0.012	0.000	0.017
is.triangulated	0.028	0.000	0.030
isKuratowskiSubgraph	0.016	0.000	0.018
isStraightLineDrawing	0.020	0.004	0.028
isomorphism	0.016	0.000	0.023
johnson.all.pairs.sp	0.016	0.000	0.021
kCliques	0.012	0.000	0.012
kCores	0.064	0.008	0.078
lambdaSets	0.008	0.000	0.014
makeBiconnectedPlanar	0.016	0.000	0.016
makeConnected	0.016	0.000	0.016
makeMaximalPlanar	0.016	0.000	0.014
maxClique	0.020	0.000	0.024
maxFlow	0.020	0.004	0.022
minCut	0.008	0.000	0.009
mstree.kruskal	0.036	0.000	0.044
mstree.prim	0.004	0.000	0.010
ordering	0.016	0.000	0.018
planarCanonicalOrdering	0.020	0.000	0.024
planarFaceTraversal	0.012	0.000	0.014
removeSelfLoops	0.016	0.004	0.024
separates	0.020	0.000	0.022
sp.between	0.048	0.004	0.058
strongComp	0.024	0.004	0.040
transClosure	0.016	0.000	0.024
transitivity	0.020	0.000	0.019
tsort	0.008	0.000	0.007
wavefront	0.012	0.000	0.015