BioC 2.14: CHECK report for RBGL on petty

Package: RBGL

Version: 1.40.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RBGL_1.40.1.tar.gz

StartedAt: 2014-10-07 23:41:44 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:45:17 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 213.1 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_1.40.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RBGL.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.40.1’
* 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 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 ... [139s/143s] 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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/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-2.14-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	1.304	0.030	1.370
astarSearch	0.014	0.001	0.016
bandwidth	0.035	0.002	0.038
bccluster	0.029	0.001	0.031
bellman.ford.sp	0.020	0.001	0.022
betweenness	0.020	0.001	0.022
bfs	0.049	0.002	0.052
biConnComp	0.019	0.001	0.020
chrobakPayneStraightLineDrawing	0.026	0.001	0.027
clusteringCoef	0.027	0.001	0.028
clusteringCoefAppr	0.021	0.001	0.022
coloring	0.015	0.001	0.017
connectedComp	0.039	0.002	0.067
dag.sp	0.022	0.002	0.024
dijkstra.sp	0.056	0.004	0.060
dominatorTree	0.017	0.002	0.018
edgeConn	0.017	0.001	0.018
edmondsMaxCardinalityMatching	0.145	0.001	0.148
edmondsOptimumBranching	0.023	0.001	0.024
extractPath	0.008	0.001	0.010
floyd.warshall.all.pairs.sp	0.020	0.001	0.022
gprofile	0.017	0.003	0.020
graphGenerator	0.002	0.001	0.002
highlyConnSG	0.025	0.004	0.029
incrConnComp	0.018	0.002	0.020
is.triangulated	0.034	0.003	0.038
isKuratowskiSubgraph	0.025	0.001	0.026
isStraightLineDrawing	0.033	0.001	0.034
isomorphism	0.028	0.002	0.031
johnson.all.pairs.sp	0.020	0.001	0.021
kCliques	0.018	0.001	0.020
kCores	0.086	0.003	0.088
lambdaSets	0.020	0.002	0.023
layout	0.002	0.000	0.002
makeBiconnectedPlanar	0.030	0.000	0.031
makeConnected	0.021	0.000	0.021
makeMaximalPlanar	0.026	0.000	0.027
maxClique	0.037	0.002	0.041
maxFlow	0.033	0.001	0.035
minCut	0.017	0.001	0.018
mstree.kruskal	0.051	0.003	0.054
mstree.prim	0.016	0.002	0.018
ordering	0.024	0.002	0.025
planarCanonicalOrdering	0.025	0.001	0.026
planarFaceTraversal	0.024	0.001	0.025
removeSelfLoops	0.026	0.002	0.027
separates	0.029	0.001	0.032
sp.between	0.059	0.002	0.061
strongComp	0.028	0.001	0.029
transClosure	0.024	0.002	0.026
transitivity	0.015	0.001	0.016
tsort	0.009	0.000	0.010
wavefront	0.018	0.001	0.020