Package: graph

Version: 1.29.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.29.2.tar.gz

StartedAt: 2011-02-24 19:41:52 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:43:25 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 93.6 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/graph.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c graph.c -o graph.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.8-bioc/meat/graph.Rcheck/graph/libs/i386
** 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	0.061	0.000	0.062
IMCA	0.392	0.013	0.407
MAPKsig	0.227	0.013	0.273
MultiGraph-class	0.071	0.002	0.074
acc-methods	0.024	0.001	0.024
addEdge	0.019	0.000	0.020
addNode	0.022	0.001	0.023
adj-methods	0.010	0.000	0.009
apoptosisGraph	0.070	0.003	0.073
attrData-class	0.003	0.001	0.003
aveNumEdges	0.019	0.000	0.020
biocRepos	0.004	0.000	0.004
boundary	0.017	0.000	0.017
buildRepDepGraph	0.000	0.001	0.001
calcProb	0	0	0
calcSumProb	0.014	0.000	0.014
clearNode	0.012	0.000	0.013
clusterGraph-class	0.007	0.001	0.007
clusteringCoefficient-methods	0.016	0.000	0.016
combineNodes	0.076	0.000	0.079
distGraph-class	0.002	0.000	0.002
duplicatedEdges	0.000	0.000	0.001
edgeMatrix	0.024	0.001	0.025
edgeSets	0.056	0.003	0.059
edgeWeights	0.017	0.000	0.017
fromGXL-methods	0.461	0.014	0.489
graph-class	0.013	0.001	0.015
graph2SparseM	0.330	0.008	0.340
graphAM-class	0.020	0.000	0.021
graphBAM-class	0.101	0.003	0.105
graphExamples	0.010	0.001	0.011
graphNEL-class	0.009	0.000	0.010
inEdges	0.006	0.000	0.006
leaves	0.025	0.002	0.027
listEdges	0.017	0.001	0.018
matrix2Graph	0.042	0.001	0.044
mostEdges	0.037	0.001	0.039
numNoEdges	0.008	0.000	0.009
pancrCaIni	0.156	0.003	0.159
randomEGraph	0.015	0.001	0.016
randomGraph	0.013	0.000	0.013
randomNodeGraph	0.009	0.000	0.010
removeEdge	0.020	0.001	0.020
removeNode	0.007	0.000	0.007
renderInfo-class	0.019	0.001	0.019
reverseEdgeDirections	0.013	0.001	0.013
simpleEdge-class	0.002	0.000	0.002
standardLabeling	0.075	0.009	0.083
subGraph	0.003	0.000	0.003
toDotR-methods	0.046	0.005	0.050
ugraph	0.019	0.001	0.020
validGraph	0.004	0.000	0.003