BioC 3.0: CHECK report for graph on perceval

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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_1.44.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/graph.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 ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.44.1’
* 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 ‘graph’ can be installed ... [7s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘package’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gxlTreeNEL: no visible global function definition for ‘xmlOutputDOM’
* 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/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [25s/25s]
 [25s/26s] 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 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c graph.c -o graph.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 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-3.0-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	0.045	0.001	0.046
IMCA	0.339	0.013	0.353
MAPKsig	0.222	0.007	0.227
MultiGraph-class	0.164	0.003	0.167
acc-methods	0.011	0.001	0.012
addEdge	0.008	0.000	0.009
addNode	0.008	0.000	0.009
adj-methods	0.004	0.001	0.004
adjacencyMatrix	0.003	0.001	0.004
apoptosisGraph	0.063	0.005	0.068
attrData-class	0.003	0.001	0.004
aveNumEdges	0.013	0.001	0.014
biocRepos	0.002	0.000	0.003
boundary	0.009	0.000	0.010
calcProb	0	0	0
calcSumProb	0.008	0.000	0.008
clearNode	0.011	0.000	0.011
clusterGraph-class	0.004	0.000	0.004
clusteringCoefficient-methods	0.009	0.000	0.009
combineNodes	0.035	0.000	0.036
distGraph-class	0.002	0.000	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.013	0.000	0.014
edgeSets	0.040	0.011	0.052
edgeWeights	0.012	0.001	0.012
fromGXL-methods	0.486	0.015	0.511
graph-class	0.012	0.002	0.014
graph2SparseM	0.186	0.008	0.194
graphAM-class	0.014	0.001	0.014
graphBAM-class	0.191	0.002	0.193
graphExamples	0.006	0.001	0.006
graphNEL-class	0.006	0.001	0.006
inEdges	0.004	0.000	0.003
leaves	0.016	0.004	0.020
listEdges	0.015	0.003	0.018
matrix2Graph	0.026	0.002	0.028
mostEdges	0.022	0.002	0.024
numNoEdges	0.007	0.001	0.007
pancrCaIni	0.130	0.004	0.215
randomEGraph	0.008	0.001	0.008
randomGraph	0.006	0.000	0.006
randomNodeGraph	0.005	0.001	0.005
removeEdge	0.011	0.000	0.012
removeNode	0.003	0.000	0.004
renderInfo-class	0.009	0.001	0.010
reverseEdgeDirections	0.007	0.000	0.006
simpleEdge-class	0.002	0.001	0.002
standardLabeling	0.056	0.004	0.061
subGraph	0.003	0.000	0.003
toDotR-methods	0.029	0.004	0.141
ugraph	0.007	0.000	0.007
validGraph	0.002	0.000	0.002

BioC 3.0: CHECK report for graph on perceval

Summary

Command output