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Package 301/389HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.24.0
Li Long
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/RBGL
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: RBGL
Version: 1.24.0
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.24.0.tar.gz
StartedAt: 2010-10-04 19:23:26 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 19:25:09 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 102.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/RBGL.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.24.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RBGL' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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: isKuratowskiSubgraph.Rd:16-17: Dropping empty section \details
prepare_Rd: isKuratowskiSubgraph.Rd:19-20: Dropping empty section \value
prepare_Rd: isomorphism.Rd:42: Dropping empty section \seealso
prepare_Rd: isStraightLineDrawing.Rd:17-18: Dropping empty section \details
prepare_Rd: isStraightLineDrawing.Rd:20-21: Dropping empty section \value
prepare_Rd: is.triangulated.Rd:43: 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 data for non-ASCII characters ... 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

RBGL.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from bbc.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c cliques.cpp -o cliques.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from cliques.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c clusteringCoef.cpp -o clusteringCoef.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from clusteringCoef.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c dominatorTree.cpp -o dominatorTree.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from dominatorTree.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c hcs.cpp -o hcs.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from hcs.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c incrConnComp.cpp -o incrConnComp.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from incrConnComp.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c interfaces.cpp -o interfaces.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from interfaces.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c layout.cpp -o layout.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from layout.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c minST.cpp -o minST.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from minST.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c mincut.cpp -o mincut.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from mincut.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c ordering.cpp -o ordering.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from ordering.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c planar.cpp -o planar.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from planar.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c shortestPath.cpp -o shortestPath.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from shortestPath.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c sna.cpp -o sna.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from sna.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c transitive_closure.cpp -o transitive_closure.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from transitive_closure.cpp:16:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c wavefront.cpp -o wavefront.o
In file included from /usr/include/c++/4.3/backward/hash_set:64,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from wavefront.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:33:2: 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 -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 layout.o minST.o mincut.o ordering.o planar.o shortestPath.o sna.o transitive_closure.o wavefront.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/RBGL.Rcheck/RBGL/libs
** 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
FileDep0.7320.0240.799
astarSearch0.0080.0000.010
bandwidth0.0240.0040.026
bccluster0.0120.0040.017
bellman.ford.sp0.0160.0000.016
betweenness0.0120.0000.014
bfs0.0280.0000.028
biConnComp0.0120.0000.012
chrobakPayneStraightLineDrawing0.020.000.02
clusteringCoef0.0160.0040.019
clusteringCoefAppr0.0120.0040.016
coloring0.0080.0040.012
connectedComp0.0280.0000.072
dag.sp0.0160.0000.016
dijkstra.sp0.0320.0040.038
dominatorTree0.0120.0000.014
edgeConn0.0080.0040.012
edmondsMaxCardinalityMatching0.0280.0000.026
edmondsOptimumBranching0.020.000.02
extractPath0.0040.0040.005
floyd.warshall.all.pairs.sp0.0120.0000.014
gprofile0.0080.0040.012
graphGenerator000
highlyConnSG0.0120.0040.016
incrConnComp0.0120.0040.014
is.triangulated0.0240.0040.026
isKuratowskiSubgraph0.0160.0000.018
isStraightLineDrawing0.0200.0000.022
isomorphism0.0240.0000.023
johnson.all.pairs.sp0.0120.0040.014
kCliques0.0160.0000.015
kCores0.1400.0080.150
lambdaSets0.0160.0000.016
layout0.0240.0040.027
makeBiconnectedPlanar0.0240.0000.023
makeConnected0.0200.0000.019
makeMaximalPlanar0.0200.0000.021
maxClique0.0240.0000.027
maxFlow0.0240.0040.025
minCut0.0160.0000.015
mstree.kruskal0.040.000.04
mstree.prim0.0120.0000.011
ordering0.020.000.02
planarCanonicalOrdering0.0160.0000.019
planarFaceTraversal0.0160.0040.017
removeSelfLoops0.0200.0000.023
separates0.0160.0040.022
sp.between0.0480.0000.045
strongComp0.0240.0000.025
transClosure0.0160.0040.018
transitivity0.0120.0000.013
tsort0.0080.0000.009
wavefront0.0120.0000.013