BioC 3.4: CHECK report for graph on morelia

Package: graph

Version: 1.52.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.52.0.tar.gz

StartedAt: 2017-04-15 03:13:13 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:14:28 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 75.2 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_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/graph.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.52.0’
* 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 ... 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
.mg_validate_node_names: no visible global function definition for
  ‘head’
MultiDiGraph: no visible global function definition for ‘head’
plot,graph-ANY: no visible global function definition for ‘getMethod’
show,MultiGraph: no visible global function definition for ‘head’
Undefined global functions or variables:
  getMethod head
Consider adding
  importFrom("methods", "getMethod")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’
 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-3.4-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/Library/Frameworks/R.framework/Resources/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-3.4-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	0.031	0.003	0.034
IMCA	0.151	0.006	0.157
MAPKsig	0.150	0.004	0.153
MultiGraph-class	0.089	0.004	0.092
acc-methods	0.013	0.001	0.013
addEdge	0.010	0.000	0.009
addNode	0.009	0.001	0.010
adj-methods	0.004	0.000	0.005
adjacencyMatrix	0.003	0.001	0.004
apoptosisGraph	0.013	0.001	0.013
attrData-class	0.003	0.000	0.003
aveNumEdges	0.010	0.000	0.009
biocRepos	0.006	0.001	0.006
boundary	0.005	0.000	0.005
calcProb	0.000	0.001	0.001
calcSumProb	0.007	0.000	0.007
clearNode	0.009	0.000	0.009
clusterGraph-class	0.004	0.000	0.004
clusteringCoefficient-methods	0.008	0.000	0.009
combineNodes	0.028	0.001	0.029
distGraph-class	0.001	0.000	0.001
duplicatedEdges	0	0	0
edgeMatrix	0.012	0.001	0.012
edgeSets	0.033	0.014	0.047
edgeWeights	0.005	0.000	0.005
fromGXL-methods	0.287	0.006	0.294
graph-class	0.006	0.001	0.005
graph2SparseM	0.095	0.004	0.099
graphAM-class	0.018	0.000	0.018
graphBAM-class	0.031	0.001	0.033
graphExamples	0.004	0.001	0.004
graphNEL-class	0.003	0.000	0.003
inEdges	0.002	0.001	0.003
leaves	0.008	0.001	0.009
listEdges	0.010	0.001	0.011
matrix2Graph	0.027	0.001	0.027
mostEdges	0.011	0.000	0.011
numNoEdges	0.005	0.000	0.005
pancrCaIni	0.095	0.002	0.097
randomEGraph	0.005	0.000	0.005
randomGraph	0.006	0.000	0.006
randomNodeGraph	0.004	0.000	0.005
removeEdge	0.009	0.000	0.009
removeNode	0.003	0.001	0.003
renderInfo-class	0.01	0.00	0.01
reverseEdgeDirections	0.006	0.001	0.007
simpleEdge-class	0.002	0.000	0.001
standardLabeling	0.047	0.002	0.049
subGraph	0.002	0.000	0.002
toDotR-methods	0.030	0.002	1.770
ugraph	0.005	0.001	0.005
validGraph	0.002	0.000	0.002