BioC 3.0: CHECK report for RBGL on perceval

Package: RBGL

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RBGL_1.42.0.tar.gz

StartedAt: 2015-04-10 05:23:28 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:26:05 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 157.8 seconds

RetCode: 0

Status:  OK

CheckDir: RBGL.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RBGL_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RBGL.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.42.0’
* 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 ... [91s/104s] 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 ... [3s/3s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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-3.0-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	0.829	0.027	0.856
astarSearch	0.008	0.001	0.009
bandwidth	0.017	0.002	0.019
bccluster	0.016	0.002	0.017
bellman.ford.sp	0.010	0.001	0.011
betweenness	0.010	0.001	0.012
bfs	0.031	0.002	0.033
biConnComp	0.009	0.001	0.010
chrobakPayneStraightLineDrawing	0.011	0.001	0.011
clusteringCoef	0.011	0.001	0.013
clusteringCoefAppr	0.013	0.001	0.013
coloring	0.007	0.001	0.009
connectedComp	0.019	0.001	0.085
dag.sp	0.012	0.001	0.014
dijkstra.sp	0.025	0.002	0.027
dominatorTree	0.008	0.001	0.009
edgeConn	0.099	0.001	0.100
edmondsMaxCardinalityMatching	0.014	0.001	0.014
edmondsOptimumBranching	0.008	0.001	0.008
extractPath	0.003	0.000	0.003
floyd.warshall.all.pairs.sp	0.010	0.001	0.010
gprofile	0.007	0.001	0.009
graphGenerator	0.001	0.000	0.001
highlyConnSG	0.013	0.003	0.017
incrConnComp	0.008	0.001	0.010
is.triangulated	0.016	0.002	0.017
isKuratowskiSubgraph	0.01	0.00	0.01
isStraightLineDrawing	0.011	0.000	0.011
isomorphism	0.015	0.002	0.017
johnson.all.pairs.sp	0.008	0.001	0.010
kCliques	0.008	0.001	0.009
kCores	0.041	0.002	0.044
lambdaSets	0.011	0.002	0.012
layout	0.001	0.000	0.001
makeBiconnectedPlanar	0.012	0.001	0.012
makeConnected	0.009	0.000	0.009
makeMaximalPlanar	0.013	0.001	0.014
maxClique	0.017	0.002	0.020
maxFlow	0.014	0.001	0.015
minCut	0.009	0.001	0.009
mstree.kruskal	0.027	0.002	0.029
mstree.prim	0.009	0.001	0.009
ordering	0.013	0.001	0.013
planarCanonicalOrdering	0.009	0.000	0.009
planarFaceTraversal	0.009	0.000	0.009
removeSelfLoops	0.014	0.001	0.015
separates	0.014	0.001	0.014
sp.between	0.028	0.001	0.030
strongComp	0.017	0.001	0.018
transClosure	0.011	0.001	0.011
transitivity	0.008	0.001	0.009
tsort	0.004	0.001	0.005
wavefront	0.009	0.001	0.010