BioC 2.14: CHECK report for graph on morelia

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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 graph_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/graph.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ 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 ‘graph’ can be installed ... [5s/5s] 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
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 ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [15s/15s]
 [15s/15s] 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/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c graph.c -o graph.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o graph.so graph.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mv graph.so BioC_graph.so
installing to /Users/biocbuild/bbs-2.14-bioc/meat/graph.Rcheck/graph/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 (graph)

name	user	system	elapsed
DFS	0.034	0.000	0.035
IMCA	0.248	0.007	0.255
MAPKsig	0.176	0.003	0.180
MultiGraph-class	0.096	0.003	0.099
acc-methods	0.063	0.001	0.063
addEdge	0.011	0.000	0.011
addNode	0.011	0.000	0.011
adj-methods	0.006	0.000	0.006
apoptosisGraph	0.032	0.002	0.034
attrData-class	0.003	0.000	0.003
aveNumEdges	0.007	0.000	0.007
biocRepos	0.002	0.000	0.003
boundary	0.007	0.001	0.007
calcProb	0.001	0.000	0.001
calcSumProb	0.007	0.000	0.007
clearNode	0.011	0.001	0.012
clusterGraph-class	0.004	0.000	0.004
clusteringCoefficient-methods	0.013	0.000	0.013
combineNodes	0.033	0.000	0.033
distGraph-class	0.001	0.000	0.002
duplicatedEdges	0.003	0.000	0.004
edgeMatrix	0.016	0.001	0.017
edgeSets	0.047	0.006	0.053
edgeWeights	0.009	0.000	0.009
fromGXL-methods	0.362	0.008	0.370
graph-class	0.008	0.001	0.009
graph2SparseM	0.137	0.003	0.140
graphAM-class	0.014	0.000	0.015
graphBAM-class	0.111	0.001	0.112
graphExamples	0.007	0.001	0.007
graphNEL-class	0.008	0.001	0.007
inEdges	0.005	0.001	0.005
leaves	0.012	0.002	0.014
listEdges	0.008	0.001	0.009
matrix2Graph	0.025	0.001	0.026
mostEdges	0.016	0.001	0.017
numNoEdges	0.004	0.000	0.004
pancrCaIni	0.140	0.003	0.143
randomEGraph	0.008	0.000	0.009
randomGraph	0.007	0.001	0.007
randomNodeGraph	0.003	0.000	0.003
removeEdge	0.012	0.000	0.012
removeNode	0.003	0.001	0.003
renderInfo-class	0.011	0.000	0.010
reverseEdgeDirections	0.007	0.000	0.007
simpleEdge-class	0.001	0.000	0.001
standardLabeling	0.064	0.002	0.065
subGraph	0.003	0.000	0.002
toDotR-methods	0.026	0.003	0.029
ugraph	0.011	0.000	0.011
validGraph	0.003	0.000	0.002

BioC 2.14: CHECK report for graph on morelia

Summary

Command output