BioC 3.4: CHECK report for graph on zin1

Package: graph

Version: 1.51.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.51.0.tar.gz

StartedAt: 2016-09-20 07:34:06 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:35:00 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 54.5 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_1.51.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/graph.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.51.0’
* 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
  ‘/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	0.024	0.000	0.023
IMCA	0.112	0.000	0.116
MAPKsig	0.128	0.000	0.128
MultiGraph-class	0.060	0.004	0.064
acc-methods	0.008	0.000	0.010
addEdge	0.008	0.000	0.006
addNode	0.008	0.000	0.006
adj-methods	0.004	0.000	0.002
adjacencyMatrix	0.000	0.000	0.003
apoptosisGraph	0.008	0.004	0.012
attrData-class	0.000	0.000	0.002
aveNumEdges	0.004	0.000	0.007
biocRepos	0.000	0.000	0.002
boundary	0.008	0.000	0.006
calcProb	0	0	0
calcSumProb	0.004	0.000	0.005
clearNode	0.004	0.000	0.007
clusterGraph-class	0.004	0.000	0.003
clusteringCoefficient-methods	0.008	0.000	0.006
combineNodes	0.016	0.004	0.019
distGraph-class	0.000	0.000	0.002
duplicatedEdges	0.000	0.000	0.001
edgeMatrix	0.008	0.000	0.009
edgeSets	0.032	0.000	0.034
edgeWeights	0.004	0.004	0.005
fromGXL-methods	0.220	0.000	0.222
graph-class	0.004	0.004	0.007
graph2SparseM	0.076	0.000	0.073
graphAM-class	0.016	0.000	0.017
graphBAM-class	0.028	0.000	0.027
graphExamples	0.000	0.000	0.004
graphNEL-class	0.000	0.000	0.003
inEdges	0.000	0.000	0.002
leaves	0.004	0.004	0.008
listEdges	0.004	0.000	0.007
matrix2Graph	0.016	0.000	0.019
mostEdges	0.012	0.000	0.012
numNoEdges	0.004	0.000	0.003
pancrCaIni	0.068	0.000	0.069
randomEGraph	0.004	0.000	0.004
randomGraph	0.008	0.000	0.006
randomNodeGraph	0.004	0.000	0.003
removeEdge	0.004	0.000	0.006
removeNode	0.004	0.000	0.003
renderInfo-class	0.008	0.000	0.005
reverseEdgeDirections	0.004	0.000	0.004
simpleEdge-class	0.000	0.000	0.001
standardLabeling	0.060	0.000	0.058
subGraph	0.004	0.000	0.001
toDotR-methods	0.020	0.000	0.021
ugraph	0.004	0.000	0.004
validGraph	0.000	0.000	0.002