BioC 3.1: CHECK report for graph on petty

Package: graph

Version: 1.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.46.0.tar.gz

StartedAt: 2015-10-08 23:29:04 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:30:54 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 109.4 seconds

RetCode: 0

Status:  OK

CheckDir: graph.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 graph_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/graph.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 ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.46.0’
* 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 ... [8s/8s] 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’
combineNodes,character-graphNEL-character : .local: no visible binding
  for global variable ‘from’
* 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 ‘graph_unit_tests.R’ [24s/24s]
 [24s/24s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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-3.1-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	0.050	0.001	0.051
IMCA	0.335	0.005	0.341
MAPKsig	0.298	0.011	0.309
MultiGraph-class	0.119	0.004	0.122
acc-methods	0.018	0.001	0.019
addEdge	0.013	0.000	0.014
addNode	0.015	0.000	0.016
adj-methods	0.007	0.000	0.007
adjacencyMatrix	0.006	0.001	0.006
apoptosisGraph	0.089	0.002	0.090
attrData-class	0.005	0.000	0.005
aveNumEdges	0.017	0.000	0.017
biocRepos	0.003	0.001	0.003
boundary	0.009	0.000	0.009
calcProb	0.000	0.000	0.001
calcSumProb	0.01	0.00	0.01
clearNode	0.017	0.001	0.018
clusterGraph-class	0.004	0.001	0.005
clusteringCoefficient-methods	0.011	0.000	0.011
combineNodes	0.045	0.001	0.046
distGraph-class	0.002	0.001	0.003
duplicatedEdges	0.001	0.000	0.001
edgeMatrix	0.025	0.001	0.026
edgeSets	0.063	0.010	0.073
edgeWeights	0.011	0.000	0.012
fromGXL-methods	0.501	0.013	0.525
graph-class	0.013	0.001	0.014
graph2SparseM	0.212	0.004	0.218
graphAM-class	0.022	0.001	0.022
graphBAM-class	0.064	0.002	0.065
graphExamples	0.008	0.001	0.008
graphNEL-class	0.005	0.000	0.005
inEdges	0.006	0.001	0.007
leaves	0.018	0.001	0.019
listEdges	0.019	0.002	0.019
matrix2Graph	0.038	0.001	0.040
mostEdges	0.029	0.001	0.030
numNoEdges	0.004	0.001	0.005
pancrCaIni	0.207	0.003	0.211
randomEGraph	0.012	0.000	0.012
randomGraph	0.010	0.001	0.011
randomNodeGraph	0.007	0.000	0.007
removeEdge	0.012	0.001	0.013
removeNode	0.006	0.001	0.007
renderInfo-class	0.017	0.001	0.017
reverseEdgeDirections	0.010	0.000	0.011
simpleEdge-class	0.002	0.000	0.003
standardLabeling	0.090	0.004	0.093
subGraph	0.004	0.000	0.005
toDotR-methods	0.066	0.004	0.077
ugraph	0.010	0.001	0.010
validGraph	0.004	0.000	0.004