BioC 3.1: CHECK report for RBGL on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RBGL_1.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RBGL.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.44.0’
* 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 ... [113s/121s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* 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 calls:
    require("methods")

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [2s/2s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/RBGL.Rcheck/00check.log’
for details.

* 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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp: In function ‘SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)’:
incrConnComp.cpp:74: warning: unused variable ‘child_index’
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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -c planar.cpp -o planar.o
planar.cpp: In function ‘SEXPREC* planarFaceTraversal(SEXPREC*, SEXPREC*, SEXPREC*)’:
planar.cpp:161: warning: comparison between signed and unsigned integer expressions
planar.cpp:165: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function ‘SEXPREC* planarCanonicalOrdering(SEXPREC*, SEXPREC*, SEXPREC*)’:
planar.cpp:256: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function ‘SEXPREC* isStraightLineDrawing(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
planar.cpp:369: warning: comparison between signed and unsigned integer expressions
planar.cpp: In function ‘SEXPREC* isKuratowskiSubgraph(SEXPREC*, SEXPREC*, SEXPREC*)’:
planar.cpp:461: warning: unused variable ‘i’
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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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/Library/Frameworks/R.framework/Resources/lib -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-3.1-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	0.787	0.019	0.816
astarSearch	0.008	0.000	0.009
bandwidth	0.027	0.001	0.028
bccluster	0.016	0.000	0.016
bellman.ford.sp	0.016	0.001	0.016
betweenness	0.014	0.001	0.015
bfs	0.031	0.002	0.032
biConnComp	0.012	0.001	0.012
chrobakPayneStraightLineDrawing	0.017	0.001	0.018
clusteringCoef	0.019	0.001	0.020
clusteringCoefAppr	0.033	0.001	0.034
coloring	0.010	0.001	0.011
connectedComp	0.025	0.002	0.063
dag.sp	0.013	0.001	0.013
dijkstra.sp	0.043	0.002	0.044
dominatorTree	0.012	0.000	0.013
edgeConn	0.014	0.001	0.014
edmondsMaxCardinalityMatching	0.034	0.001	0.036
edmondsOptimumBranching	0.016	0.000	0.016
extractPath	0.006	0.000	0.006
floyd.warshall.all.pairs.sp	0.015	0.001	0.016
gprofile	0.011	0.000	0.011
graphGenerator	0.002	0.000	0.002
highlyConnSG	0.116	0.001	0.117
incrConnComp	0.012	0.001	0.013
is.triangulated	0.018	0.001	0.019
isKuratowskiSubgraph	0.016	0.001	0.017
isStraightLineDrawing	0.019	0.001	0.020
isomorphism	0.021	0.003	0.023
johnson.all.pairs.sp	0.011	0.002	0.013
kCliques	0.011	0.002	0.013
kCores	0.151	0.005	0.156
lambdaSets	0.012	0.001	0.013
layout	0.002	0.000	0.002
makeBiconnectedPlanar	0.020	0.000	0.021
makeConnected	0.014	0.000	0.014
makeMaximalPlanar	0.016	0.001	0.017
maxClique	0.023	0.001	0.024
maxFlow	0.022	0.003	0.025
minCut	0.010	0.002	0.011
mstree.kruskal	0.029	0.005	0.034
mstree.prim	0.010	0.001	0.012
ordering	0.018	0.003	0.021
planarCanonicalOrdering	0.016	0.002	0.018
planarFaceTraversal	0.012	0.000	0.013
removeSelfLoops	0.016	0.000	0.016
separates	0.022	0.000	0.022
sp.between	0.047	0.002	0.050
strongComp	0.023	0.000	0.023
transClosure	0.012	0.000	0.013
transitivity	0.011	0.000	0.011
tsort	0.006	0.001	0.008
wavefront	0.013	0.001	0.013

BioC 3.1: CHECK report for RBGL on petty

Summary

Command output