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Package 336/436HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.27.1
Li Long
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RBGL
Last Changed Rev: 51054 / Revision: 53255
Last Changed Date: 2010-11-25 03:18:39 -0800 (Thu, 25 Nov 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  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 
petty Mac OS X Snow Leopard (10.6.4) / i386  ERROR  skipped  skipped 

Summary

Package: RBGL
Version: 1.27.1
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.27.1.tar.gz
StartedAt: 2011-02-24 22:07:08 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 22:08:48 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 100.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/RBGL.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.27.1’
* 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: 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 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:

* installing *source* package ‘RBGL’ ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from bbc.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c cliques.cpp -o cliques.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from cliques.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c clusteringCoef.cpp -o clusteringCoef.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from clusteringCoef.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c dominatorTree.cpp -o dominatorTree.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from dominatorTree.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-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++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c hcs.cpp -o hcs.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from hcs.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c incrConnComp.cpp -o incrConnComp.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from incrConnComp.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c interfaces.cpp -o interfaces.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from interfaces.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c layout.cpp -o layout.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from layout.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c minST.cpp -o minST.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from minST.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c mincut.cpp -o mincut.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from mincut.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c ordering.cpp -o ordering.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from ordering.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c planar.cpp -o planar.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from planar.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c shortestPath.cpp -o shortestPath.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from shortestPath.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c sna.cpp -o sna.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from sna.cpp:1:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-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++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from transitive_closure.cpp:16:
/usr/include/c++/4.4/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/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c wavefront.cpp -o wavefront.o
In file included from /usr/include/c++/4.4/backward/hash_set:59,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from wavefront.cpp:1:
/usr/include/c++/4.4/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 -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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-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
FileDep0.6240.0160.647
astarSearch0.0080.0000.009
bandwidth0.0240.0000.022
bccluster0.0160.0000.016
bellman.ford.sp0.0120.0000.014
betweenness0.0120.0000.013
bfs0.0280.0000.026
biConnComp0.0120.0000.013
chrobakPayneStraightLineDrawing0.0160.0000.015
clusteringCoef0.020.000.02
clusteringCoefAppr0.0840.0000.086
coloring0.0080.0000.009
connectedComp0.0320.0040.070
dag.sp0.0160.0000.017
dijkstra.sp0.0320.0040.037
dominatorTree0.0160.0000.017
edgeConn0.0080.0000.011
edmondsMaxCardinalityMatching0.0240.0000.022
edmondsOptimumBranching0.0120.0040.013
extractPath0.0040.0000.005
floyd.warshall.all.pairs.sp0.0080.0080.013
gprofile0.0120.0000.015
graphGenerator0.0000.0000.001
highlyConnSG0.0160.0000.014
incrConnComp0.0160.0000.016
is.triangulated0.0240.0040.026
isKuratowskiSubgraph0.0160.0000.017
isStraightLineDrawing0.0240.0000.024
isomorphism0.0160.0000.018
johnson.all.pairs.sp0.0120.0000.013
kCliques0.0080.0040.013
kCores0.0600.0000.067
lambdaSets0.0160.0000.019
layout0.0200.0000.024
makeBiconnectedPlanar0.0240.0000.026
makeConnected0.0120.0000.015
makeMaximalPlanar0.0200.0000.024
maxClique0.0200.0000.023
maxFlow0.0240.0000.025
minCut0.0120.0000.011
mstree.kruskal0.0360.0000.039
mstree.prim0.0080.0040.012
ordering0.0200.0000.021
planarCanonicalOrdering0.0120.0000.012
planarFaceTraversal0.0160.0000.016
removeSelfLoops0.020.000.02
separates0.0160.0040.022
sp.between0.0440.0000.042
strongComp0.0160.0040.020
transClosure0.0160.0040.017
transitivity0.0120.0000.010
tsort0.0040.0000.006
wavefront0.0080.0000.011