Package: RBGL

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RBGL_1.35.0.tar.gz

StartedAt: 2013-03-24 09:17:30 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:20:38 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 187.1 seconds

RetCode: 0

Status:  OK

CheckDir: RBGL.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RBGL.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.35.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'RBGL' can be installed ... [119s/127s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... OK
* 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [5s/6s] OK
* checking for unstated dependencies in vignettes ... OK
* 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

* installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c bbc.cpp -o bbc.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c cliques.cpp -o cliques.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c clusteringCoef.cpp -o clusteringCoef.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c dominatorTree.cpp -o dominatorTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c hcs.cpp -o hcs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c incrConnComp.cpp -o incrConnComp.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c interfaces.cpp -o interfaces.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c minST.cpp -o minST.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c mincut.cpp -o mincut.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c ordering.cpp -o ordering.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c planar.cpp -o planar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c shortestPath.cpp -o shortestPath.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c sna.cpp -o sna.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c transitive_closure.cpp -o transitive_closure.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fPIC  -mtune=core2 -g -O2  -c wavefront.cpp -o wavefront.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-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	0.933	0.036	0.996
astarSearch	0.022	0.002	0.024
bandwidth	0.040	0.002	0.041
bccluster	0.029	0.002	0.031
bellman.ford.sp	0.025	0.003	0.029
betweenness	0.028	0.003	0.031
bfs	0.166	0.006	0.174
biConnComp	0.021	0.003	0.025
chrobakPayneStraightLineDrawing	0.042	0.007	0.051
clusteringCoef	0.032	0.004	0.037
clusteringCoefAppr	0.032	0.004	0.036
coloring	0.025	0.003	0.027
connectedComp	0.040	0.004	0.063
dag.sp	0.025	0.003	0.028
dijkstra.sp	0.057	0.005	0.070
dominatorTree	0.029	0.002	0.035
edgeConn	0.024	0.004	0.030
edmondsMaxCardinalityMatching	0.064	0.009	0.077
edmondsOptimumBranching	0.025	0.003	0.029
extractPath	0.014	0.002	0.021
floyd.warshall.all.pairs.sp	0.021	0.003	0.028
gprofile	0.020	0.003	0.023
graphGenerator	0.009	0.002	0.013
highlyConnSG	0.029	0.003	0.035
incrConnComp	0.026	0.003	0.031
is.triangulated	0.044	0.005	0.051
isKuratowskiSubgraph	0.048	0.003	0.059
isStraightLineDrawing	0.042	0.006	0.058
isomorphism	0.031	0.005	0.036
johnson.all.pairs.sp	0.021	0.003	0.028
kCliques	0.021	0.003	0.027
kCores	0.081	0.006	0.095
lambdaSets	0.030	0.002	0.036
layout	0.015	0.002	0.018
makeBiconnectedPlanar	0.041	0.004	0.055
makeConnected	0.033	0.004	0.049
makeMaximalPlanar	0.035	0.004	0.040
maxClique	0.040	0.006	0.058
maxFlow	0.039	0.004	0.051
minCut	0.023	0.002	0.029
mstree.kruskal	0.059	0.006	0.081
mstree.prim	0.020	0.004	0.025
ordering	0.031	0.004	0.045
planarCanonicalOrdering	0.034	0.005	0.046
planarFaceTraversal	0.034	0.005	0.042
removeSelfLoops	0.030	0.004	0.041
separates	0.032	0.004	0.054
sp.between	0.062	0.005	0.086
strongComp	0.036	0.003	0.048
transClosure	0.026	0.002	0.030
transitivity	0.025	0.002	0.027
tsort	0.016	0.003	0.031
wavefront	0.028	0.004	0.040