Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

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

Summary

Package: RBGL
Version: 1.28.0
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.28.0.tar.gz
StartedAt: 2011-10-20 14:07:23 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:09:39 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 136.0 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 2.13.2 (2011-09-30)
* 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 ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘RBGL’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
* 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: astarSearch.Rd:14-15: Dropping empty section \value
prepare_Rd: astarSearch.Rd:27: Dropping empty section \seealso
prepare_Rd: bandwidth.Rd:36: Dropping empty section \seealso
prepare_Rd: biConnComp.Rd:52: Dropping empty section \seealso
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:16-17: Dropping empty section \details
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:19-20: Dropping empty section \value
prepare_Rd: boyerMyrvoldPlanarityTest.Rd:33-34: Dropping empty section \examples
prepare_Rd: chrobakPayneStraightLineDrawing.Rd:16-17: Dropping empty section \details
prepare_Rd: chrobakPayneStraightLineDrawing.Rd:19-20: Dropping empty section \value
prepare_Rd: coloring.Rd:42: Dropping empty section \seealso
prepare_Rd: dominatorTree.Rd:37: Dropping empty section \seealso
prepare_Rd: edmondsMaxCardinalityMatching.Rd:16-17: Dropping empty section \details
prepare_Rd: edmondsMaxCardinalityMatching.Rd:19-20: Dropping empty section \value
prepare_Rd: edmondsOptimumBranching.Rd:20-21: Dropping empty section \value
prepare_Rd: gprofile.Rd:37: Dropping empty section \seealso
prepare_Rd: is.triangulated.Rd:43: Dropping empty section \seealso
prepare_Rd: isKuratowskiSubgraph.Rd:16-17: Dropping empty section \details
prepare_Rd: isKuratowskiSubgraph.Rd:19-20: Dropping empty section \value
prepare_Rd: isStraightLineDrawing.Rd:17-18: Dropping empty section \details
prepare_Rd: isStraightLineDrawing.Rd:20-21: Dropping empty section \value
prepare_Rd: isomorphism.Rd:42: Dropping empty section \seealso
prepare_Rd: johnson.all.pairs.sp.Rd:34: Dropping empty section \note
prepare_Rd: kCliques.Rd:45: Dropping empty section \seealso
prepare_Rd: kCores.Rd:39: Dropping empty section \seealso
prepare_Rd: lambdaSets.Rd:45: Dropping empty section \seealso
prepare_Rd: makeBiconnectedPlanar.Rd:16-17: Dropping empty section \details
prepare_Rd: makeBiconnectedPlanar.Rd:19-20: Dropping empty section \value
prepare_Rd: makeConnected.Rd:16-17: Dropping empty section \details
prepare_Rd: makeConnected.Rd:19-20: Dropping empty section \value
prepare_Rd: makeMaximalPlanar.Rd:16-17: Dropping empty section \details
prepare_Rd: makeMaximalPlanar.Rd:19-20: Dropping empty section \value
prepare_Rd: maxClique.Rd:35: Dropping empty section \seealso
prepare_Rd: maximumCycleRatio.Rd:16-17: Dropping empty section \details
prepare_Rd: maximumCycleRatio.Rd:19-20: Dropping empty section \value
prepare_Rd: maximumCycleRatio.Rd:33-34: Dropping empty section \examples
prepare_Rd: minimumCycleRatio.Rd:16-17: Dropping empty section \details
prepare_Rd: minimumCycleRatio.Rd:19-20: Dropping empty section \value
prepare_Rd: minimumCycleRatio.Rd:33-34: Dropping empty section \examples
prepare_Rd: ordering.Rd:77: Dropping empty section \seealso
prepare_Rd: planarCanonicalOrdering.Rd:16-17: Dropping empty section \details
prepare_Rd: planarCanonicalOrdering.Rd:19-20: Dropping empty section \value
prepare_Rd: planarFaceTraversal.Rd:16-17: Dropping empty section \details
prepare_Rd: planarFaceTraversal.Rd:19-20: Dropping empty section \value
prepare_Rd: removeSelfLoops.Rd:27: Dropping empty section \seealso
prepare_Rd: sloanStartEndVertices.Rd:16-17: Dropping empty section \details
prepare_Rd: sloanStartEndVertices.Rd:19-20: Dropping empty section \value
prepare_Rd: sloanStartEndVertices.Rd:33-34: Dropping empty section \examples
prepare_Rd: transClosure.Rd:36: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: XML
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

RBGL.Rcheck/00install.out:

* installing *source* package ‘RBGL’ ...
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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from bbc.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from cliques.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from clusteringCoef.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from dominatorTree.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from edmonds_optimum_branching.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from hcs.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from incrConnComp.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from interfaces.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from layout.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from minST.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from mincut.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from ordering.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from planar.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from shortestPath.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from sna.cpp:1:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from transitive_closure.cpp:16:
/usr/include/c++/4.5/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++/4.5/backward/hash_set:60:0,
                 from boostIncl/boost/graph/adjacency_list.hpp:25,
                 from RBGL.hpp:26,
                 from wavefront.cpp:1:
/usr/include/c++/4.5/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
FileDep0.9440.0160.962
astarSearch0.0080.0000.011
bandwidth0.0240.0000.026
bccluster0.0160.0000.018
bellman.ford.sp0.0160.0000.018
betweenness0.0160.0000.014
bfs0.0280.0000.030
biConnComp0.0120.0000.013
chrobakPayneStraightLineDrawing0.0200.0000.018
clusteringCoef0.0160.0000.017
clusteringCoefAppr0.0160.0040.017
coloring0.0080.0040.011
connectedComp0.0280.0000.045
dag.sp0.0160.0000.018
dijkstra.sp0.0440.0000.044
dominatorTree0.0120.0040.016
edgeConn0.0120.0000.012
edmondsMaxCardinalityMatching0.0240.0000.025
edmondsOptimumBranching0.0160.0000.017
extractPath0.0040.0000.006
floyd.warshall.all.pairs.sp0.0160.0000.014
gprofile0.0120.0000.013
graphGenerator0.0040.0000.000
highlyConnSG0.0160.0000.016
incrConnComp0.0160.0000.015
is.triangulated0.0240.0000.024
isKuratowskiSubgraph0.0200.0000.018
isStraightLineDrawing0.0160.0040.020
isomorphism0.0200.0040.020
johnson.all.pairs.sp0.0160.0040.020
kCliques0.0120.0000.012
kCores0.0720.0000.070
lambdaSets0.0200.0000.018
layout0.0240.0000.026
makeBiconnectedPlanar0.0240.0000.024
makeConnected0.020.000.02
makeMaximalPlanar0.0240.0000.023
maxClique0.0240.0000.027
maxFlow0.0280.0000.028
minCut0.0120.0040.017
mstree.kruskal0.0400.0040.044
mstree.prim0.0040.0080.013
ordering0.0160.0040.019
planarCanonicalOrdering0.0160.0000.013
planarFaceTraversal0.0160.0000.016
removeSelfLoops0.0240.0000.024
separates0.0240.0040.024
sp.between0.0440.0000.044
strongComp0.0320.0000.028
transClosure0.0120.0040.018
transitivity0.0120.0000.014
tsort0.0080.0000.006
wavefront0.0080.0040.012