Package: graph

Version: 1.31.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.31.1.tar.gz

StartedAt: 2011-07-07 00:55:55 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 00:57:05 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 70.1 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/graph.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.31.1’
* 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 installed package size ... 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 ... 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o graph.so graph.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/graph.Rcheck/graph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘GraphClass.Rnw’ 
   ‘MultiGraphClass.Rnw’ 
   ‘clusterGraph.Rnw’ 
   ‘graph.Rnw’ 
   ‘graphAttributes.Rnw’ 
** testing if installed package can be loaded

* DONE (graph)

name	user	system	elapsed
DFS	0.052	0.000	0.051
IMCA	0.296	0.012	0.312
MAPKsig	0.156	0.020	0.175
MultiGraph-class	0.116	0.008	0.120
acc-methods	0.020	0.000	0.021
addEdge	0.016	0.000	0.014
addNode	0.016	0.000	0.015
adj-methods	0.004	0.000	0.007
apoptosisGraph	0.028	0.004	0.032
attrData-class	0.004	0.000	0.001
aveNumEdges	0.012	0.000	0.013
biocRepos	0.004	0.000	0.002
boundary	0.012	0.000	0.011
buildRepDepGraph	0	0	0
calcProb	0	0	0
calcSumProb	0.008	0.000	0.009
clearNode	0.012	0.000	0.009
clusterGraph-class	0.004	0.004	0.007
clusteringCoefficient-methods	0.008	0.004	0.011
combineNodes	0.06	0.00	0.06
distGraph-class	0.004	0.000	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.016	0.000	0.018
edgeSets	0.028	0.004	0.033
edgeWeights	0.012	0.000	0.013
fromGXL-methods	0.504	0.004	0.513
graph-class	0.012	0.000	0.010
graph2SparseM	0.276	0.004	0.279
graphAM-class	0.028	0.000	0.026
graphBAM-class	0.148	0.000	0.149
graphExamples	0.008	0.004	0.009
graphNEL-class	0.004	0.000	0.006
inEdges	0.004	0.000	0.006
leaves	0.020	0.000	0.017
listEdges	0.012	0.000	0.013
matrix2Graph	0.032	0.000	0.032
mostEdges	0.020	0.004	0.027
numNoEdges	0.004	0.000	0.005
pancrCaIni	0.088	0.004	0.093
randomEGraph	0.016	0.000	0.016
randomGraph	0.008	0.000	0.009
randomNodeGraph	0.004	0.000	0.007
removeEdge	0.008	0.004	0.013
removeNode	0.008	0.000	0.009
renderInfo-class	0.012	0.000	0.013
reverseEdgeDirections	0.008	0.000	0.008
simpleEdge-class	0.004	0.000	0.002
standardLabeling	0.068	0.000	0.068
subGraph	0.000	0.004	0.002
toDotR-methods	0.040	0.004	0.042
ugraph	0.016	0.000	0.017
validGraph	0.004	0.000	0.002