BioC 3.3: CHECK report for graph on linux2.bioconductor.org

Package: graph

Version: 1.49.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.49.1.tar.gz

StartedAt: 2015-10-27 04:34:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:35:28 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 57.6 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.49.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/graph.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.49.1’
* 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 ... [3s/3s] 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 ... OK
* 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [15s/15s]
 [15s/15s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-3.3-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	0.033	0.000	0.033
IMCA	0.183	0.000	0.183
MAPKsig	0.154	0.003	0.158
MultiGraph-class	0.083	0.004	0.087
acc-methods	0.013	0.000	0.013
addEdge	0.009	0.000	0.009
addNode	0.009	0.000	0.009
adj-methods	0.005	0.000	0.005
adjacencyMatrix	0.004	0.000	0.004
apoptosisGraph	0.015	0.003	0.019
attrData-class	0.003	0.000	0.003
aveNumEdges	0.013	0.000	0.013
biocRepos	0.002	0.000	0.002
boundary	0.007	0.000	0.007
calcProb	0.001	0.000	0.001
calcSumProb	0.007	0.000	0.007
clearNode	0.01	0.00	0.01
clusterGraph-class	0.004	0.000	0.004
clusteringCoefficient-methods	0.009	0.000	0.009
combineNodes	0.032	0.000	0.032
distGraph-class	0.000	0.000	0.002
duplicatedEdges	0.001	0.001	0.000
edgeMatrix	0.014	0.000	0.014
edgeSets	0.051	0.000	0.051
edgeWeights	0.008	0.000	0.008
fromGXL-methods	0.322	0.000	0.322
graph-class	0.009	0.000	0.009
graph2SparseM	0.109	0.004	0.114
graphAM-class	0.014	0.000	0.014
graphBAM-class	0.043	0.000	0.043
graphExamples	0.006	0.000	0.006
graphNEL-class	0.005	0.000	0.005
inEdges	0.003	0.000	0.003
leaves	0.014	0.000	0.014
listEdges	0.008	0.000	0.008
matrix2Graph	0.018	0.000	0.018
mostEdges	0.01	0.00	0.01
numNoEdges	0.004	0.000	0.004
pancrCaIni	0.058	0.004	0.063
randomEGraph	0.004	0.000	0.004
randomGraph	0.004	0.000	0.004
randomNodeGraph	0.002	0.000	0.002
removeEdge	0.005	0.000	0.005
removeNode	0.002	0.000	0.002
renderInfo-class	0.006	0.000	0.006
reverseEdgeDirections	0.003	0.000	0.003
simpleEdge-class	0.001	0.000	0.001
standardLabeling	0.054	0.000	0.054
subGraph	0.001	0.000	0.001
toDotR-methods	0.087	0.000	0.087
ugraph	0.004	0.000	0.004
validGraph	0.001	0.000	0.001