BioC 3.5: CHECK report for graph on veracruz2

Package: graph

Version: 1.54.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.54.0.tar.gz

StartedAt: 2017-10-18 04:32:32 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:33:42 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 70.6 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_1.54.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/graph.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.54.0’
* 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-3.5-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   -fPIC  -Wall -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-3.5-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	0.054	0.003	0.057
IMCA	0.107	0.004	0.114
MAPKsig	0.342	0.008	0.354
MultiGraph-class	0.611	0.006	0.648
acc-methods	0.096	0.001	0.098
addEdge	0.052	0.001	0.063
addNode	0.023	0.000	0.024
adj-methods	0.003	0.000	0.003
adjacencyMatrix	0.002	0.000	0.003
apoptosisGraph	0.014	0.002	0.016
attrData-class	0.003	0.000	0.003
aveNumEdges	0.003	0.000	0.004
biocRepos	0.001	0.001	0.003
boundary	0.006	0.000	0.006
calcProb	0.000	0.000	0.001
calcSumProb	0.063	0.001	0.066
clearNode	0.012	0.000	0.012
clusterGraph-class	0.006	0.001	0.007
clusteringCoefficient-methods	0.032	0.000	0.032
combineNodes	0.118	0.001	0.120
distGraph-class	0.002	0.000	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.037	0.001	0.038
edgeSets	0.037	0.005	0.045
edgeWeights	0.012	0.001	0.012
fromGXL-methods	0.452	0.011	0.473
graph-class	0.007	0.001	0.008
graph2SparseM	0.086	0.003	0.090
graphAM-class	0.035	0.001	0.036
graphBAM-class	0.262	0.002	0.267
graphExamples	0.003	0.000	0.005
graphNEL-class	0.007	0.000	0.007
inEdges	0.006	0.000	0.007
leaves	0.008	0.002	0.010
listEdges	0.011	0.001	0.012
matrix2Graph	0.032	0.001	0.034
mostEdges	0.007	0.000	0.007
numNoEdges	0.002	0.000	0.003
pancrCaIni	0.181	0.003	0.190
randomEGraph	0.004	0.000	0.004
randomGraph	0.004	0.000	0.004
randomNodeGraph	0.002	0.000	0.003
removeEdge	0.046	0.001	0.047
removeNode	0.007	0.000	0.007
renderInfo-class	0.057	0.001	0.059
reverseEdgeDirections	0.003	0.000	0.004
simpleEdge-class	0.001	0.000	0.001
standardLabeling	0.048	0.002	0.050
subGraph	0.001	0.000	0.002
toDotR-methods	0.036	0.002	0.039
ugraph	0.008	0.000	0.009
validGraph	0.001	0.000	0.001