BioC 2.12: CHECK report for RBGL on petty

Package: RBGL

Version: 1.36.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RBGL_1.36.2.tar.gz

StartedAt: 2013-10-08 23:36:31 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:39:58 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 207.7 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 3.0.1 (2013-05-16)
* 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 '1.36.2'
* 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 ... [138s/141s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [6s/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 -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
** testing if installed package can be loaded
* DONE (RBGL)

name	user	system	elapsed
FileDep	1.170	0.036	1.217
astarSearch	0.023	0.002	0.024
bandwidth	0.048	0.002	0.051
bccluster	0.037	0.003	0.041
bellman.ford.sp	0.030	0.002	0.032
betweenness	0.027	0.002	0.029
bfs	0.057	0.004	0.061
biConnComp	0.029	0.001	0.030
chrobakPayneStraightLineDrawing	0.046	0.001	0.048
clusteringCoef	0.036	0.002	0.038
clusteringCoefAppr	0.031	0.002	0.032
coloring	0.020	0.001	0.022
connectedComp	0.042	0.003	0.095
dag.sp	0.027	0.002	0.029
dijkstra.sp	0.056	0.003	0.060
dominatorTree	0.028	0.001	0.029
edgeConn	0.023	0.001	0.024
edmondsMaxCardinalityMatching	0.070	0.002	0.072
edmondsOptimumBranching	0.032	0.002	0.035
extractPath	0.019	0.001	0.020
floyd.warshall.all.pairs.sp	0.027	0.002	0.030
gprofile	0.024	0.002	0.026
graphGenerator	0.01	0.00	0.01
highlyConnSG	0.030	0.002	0.032
incrConnComp	0.029	0.002	0.032
is.triangulated	0.049	0.003	0.053
isKuratowskiSubgraph	0.054	0.002	0.056
isStraightLineDrawing	0.050	0.001	0.051
isomorphism	0.038	0.003	0.041
johnson.all.pairs.sp	0.026	0.001	0.028
kCliques	0.026	0.002	0.028
kCores	0.112	0.005	0.116
lambdaSets	0.034	0.002	0.036
layout	0.020	0.001	0.020
makeBiconnectedPlanar	0.046	0.001	0.047
makeConnected	0.038	0.001	0.039
makeMaximalPlanar	0.046	0.001	0.048
maxClique	0.047	0.003	0.051
maxFlow	0.046	0.002	0.047
minCut	0.133	0.002	0.136
mstree.kruskal	0.066	0.003	0.070
mstree.prim	0.025	0.002	0.026
ordering	0.037	0.002	0.040
planarCanonicalOrdering	0.035	0.001	0.036
planarFaceTraversal	0.036	0.001	0.037
removeSelfLoops	0.033	0.002	0.034
separates	0.035	0.002	0.037
sp.between	0.075	0.004	0.080
strongComp	0.044	0.002	0.046
transClosure	0.034	0.002	0.036
transitivity	0.024	0.002	0.026
tsort	0.018	0.001	0.019
wavefront	0.029	0.002	0.031