BioC 3.4: CHECK report for graph on malbec1

Package: graph

Version: 1.52.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.52.0.tar.gz

StartedAt: 2017-04-14 23:02:03 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:03:04 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 60.9 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.52.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/graph.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/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	0.020	0.000	0.019
IMCA	0.108	0.008	0.113
MAPKsig	0.160	0.000	0.159
MultiGraph-class	0.052	0.004	0.056
acc-methods	0.008	0.000	0.010
addEdge	0.008	0.000	0.006
addNode	0.004	0.000	0.005
adj-methods	0.000	0.000	0.003
adjacencyMatrix	0.000	0.000	0.002
apoptosisGraph	0.012	0.000	0.012
attrData-class	0.000	0.000	0.002
aveNumEdges	0.008	0.000	0.007
biocRepos	0.004	0.000	0.001
boundary	0.004	0.000	0.006
calcProb	0	0	0
calcSumProb	0.004	0.000	0.004
clearNode	0.008	0.000	0.007
clusterGraph-class	0.004	0.000	0.003
clusteringCoefficient-methods	0.004	0.000	0.006
combineNodes	0.02	0.00	0.02
distGraph-class	0.000	0.000	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.008	0.000	0.008
edgeSets	0.032	0.000	0.034
edgeWeights	0.004	0.000	0.004
fromGXL-methods	0.224	0.004	0.229
graph-class	0.004	0.004	0.005
graph2SparseM	0.068	0.000	0.068
graphAM-class	0.012	0.004	0.015
graphBAM-class	0.024	0.000	0.026
graphExamples	0.004	0.000	0.003
graphNEL-class	0.004	0.000	0.003
inEdges	0.004	0.000	0.003
leaves	0.008	0.000	0.008
listEdges	0.008	0.000	0.006
matrix2Graph	0.016	0.000	0.018
mostEdges	0.008	0.000	0.010
numNoEdges	0.004	0.000	0.003
pancrCaIni	0.064	0.000	0.064
randomEGraph	0.008	0.000	0.005
randomGraph	0.004	0.000	0.005
randomNodeGraph	0.004	0.000	0.003
removeEdge	0.008	0.000	0.005
removeNode	0.000	0.000	0.002
renderInfo-class	0.008	0.000	0.005
reverseEdgeDirections	0.004	0.000	0.004
simpleEdge-class	0.000	0.000	0.001
standardLabeling	0.048	0.004	0.051
subGraph	0.004	0.000	0.002
toDotR-methods	0.020	0.000	0.018
ugraph	0.004	0.000	0.005
validGraph	0.000	0.000	0.002