Package: graph

Version: 1.29.2

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.29.2.tar.gz

StartedAt: 2011-02-24 20:12:56 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:14:06 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 70.1 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/graph.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.29.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘graph’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* 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 ... NOTE
'library' or 'require' call not declared from: Rgraphviz
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o graph.so graph.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/graph.Rcheck/graph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (graph)

name	user	system	elapsed
DFS	0.044	0.000	0.046
IMCA	0.264	0.016	0.283
MAPKsig	0.176	0.008	0.256
MultiGraph-class	0.048	0.000	0.047
acc-methods	0.016	0.000	0.016
addEdge	0.012	0.000	0.013
addNode	0.016	0.000	0.013
adj-methods	0.008	0.000	0.006
apoptosisGraph	0.036	0.008	0.048
attrData-class	0.000	0.004	0.002
aveNumEdges	0.012	0.000	0.013
biocRepos	0.000	0.000	0.002
boundary	0.016	0.000	0.014
buildRepDepGraph	0	0	0
calcProb	0	0	0
calcSumProb	0.008	0.000	0.010
clearNode	0.012	0.000	0.010
clusterGraph-class	0.004	0.000	0.005
clusteringCoefficient-methods	0.012	0.000	0.011
combineNodes	0.056	0.000	0.056
distGraph-class	0.000	0.000	0.001
duplicatedEdges	0	0	0
edgeMatrix	0.016	0.000	0.017
edgeSets	0.024	0.004	0.031
edgeWeights	0.008	0.000	0.010
fromGXL-methods	0.388	0.016	0.401
graph-class	0.008	0.004	0.010
graph2SparseM	0.188	0.016	0.205
graphAM-class	0.096	0.000	0.096
graphBAM-class	0.076	0.004	0.084
graphExamples	0.012	0.004	0.021
graphNEL-class	0.008	0.004	0.022
inEdges	0.004	0.000	0.005
leaves	0.020	0.000	0.022
listEdges	0.008	0.000	0.012
matrix2Graph	0.028	0.000	0.027
mostEdges	0.028	0.000	0.026
numNoEdges	0.004	0.000	0.006
pancrCaIni	0.112	0.000	0.113
randomEGraph	0.012	0.000	0.009
randomGraph	0.008	0.000	0.009
randomNodeGraph	0.008	0.000	0.006
removeEdge	0.012	0.000	0.012
removeNode	0.004	0.000	0.005
renderInfo-class	0.012	0.000	0.013
reverseEdgeDirections	0.008	0.000	0.010
simpleEdge-class	0.004	0.000	0.001
standardLabeling	0.060	0.000	0.059
subGraph	0.000	0.004	0.002
toDotR-methods	0.024	0.004	0.030
ugraph	0.016	0.000	0.015
validGraph	0.004	0.000	0.003