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Package 402/514HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.30.1
Bioconductor Package Maintainer
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/RBGL
Last Changed Rev: 60128 / Revision: 64395
Last Changed Date: 2011-11-08 10:06:01 -0800 (Tue, 08 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  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: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.30.1.tar.gz
StartedAt: 2012-03-24 02:14:13 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:16:27 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 133.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/RBGL.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.30.1’
* 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 ... NOTE
  installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
* 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 ... 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 ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/RBGL.Rcheck/RBGL/libs/RBGL.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__assert_fail’, 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’ ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/RBGL.Rcheck/RBGL/libs
** 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
FileDep0.7600.0400.798
astarSearch0.0040.0040.008
bandwidth0.020.000.02
bccluster0.0080.0080.020
bellman.ford.sp0.0120.0000.014
betweenness0.0080.0000.011
bfs0.0200.0000.021
biConnComp0.0080.0040.015
chrobakPayneStraightLineDrawing0.0200.0000.018
clusteringCoef0.0200.0000.018
clusteringCoefAppr0.0160.0040.019
coloring0.0080.0000.011
connectedComp0.0320.0040.053
dag.sp0.0120.0040.017
dijkstra.sp0.0480.0000.045
dominatorTree0.0120.0000.013
edgeConn0.0120.0000.013
edmondsMaxCardinalityMatching0.0320.0000.030
edmondsOptimumBranching0.0160.0000.016
extractPath0.0080.0000.007
floyd.warshall.all.pairs.sp0.0200.0000.019
gprofile0.0120.0000.012
graphGenerator000
highlyConnSG0.0160.0000.017
incrConnComp0.0160.0000.014
is.triangulated0.0280.0000.029
isKuratowskiSubgraph0.0160.0000.019
isStraightLineDrawing0.0200.0000.022
isomorphism0.0160.0040.023
johnson.all.pairs.sp0.0120.0040.015
kCliques0.0160.0000.018
kCores0.0680.0080.077
lambdaSets0.0200.0000.021
layout0.0240.0040.025
makeBiconnectedPlanar0.0240.0000.026
makeConnected0.0160.0000.016
makeMaximalPlanar0.0240.0000.023
maxClique0.0240.0040.027
maxFlow0.0240.0040.029
minCut0.0120.0000.013
mstree.kruskal0.0400.0040.045
mstree.prim0.0160.0000.023
ordering0.0200.0040.025
planarCanonicalOrdering0.0120.0040.015
planarFaceTraversal0.0160.0000.016
removeSelfLoops0.0240.0000.025
separates0.0200.0040.024
sp.between0.0520.0000.050
strongComp0.0320.0040.035
transClosure0.0200.0000.018
transitivity0.0120.0040.015
tsort0.0040.0000.005
wavefront0.0080.0000.011