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: 2011-05-09 12:48:46 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:49:58 -0700 (Mon, 09 May 2011)

EllapsedTime: 71.8 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) (2011-04-18 r55504)
* 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	0.092	0.000	0.091
IMCA	0.188	0.028	0.310
MAPKsig	0.160	0.008	0.170
MultiGraph-class	0.108	0.000	0.110
acc-methods	0.024	0.000	0.022
addEdge	0.016	0.000	0.013
addNode	0.016	0.000	0.015
adj-methods	0.004	0.000	0.006
apoptosisGraph	0.028	0.000	0.031
attrData-class	0.000	0.000	0.002
aveNumEdges	0.016	0.000	0.016
biocRepos	0.000	0.000	0.002
boundary	0.008	0.000	0.009
buildRepDepGraph	0	0	0
calcProb	0	0	0
calcSumProb	0.012	0.000	0.012
clearNode	0.008	0.000	0.008
clusterGraph-class	0.004	0.000	0.005
clusteringCoefficient-methods	0.012	0.000	0.013
combineNodes	0.056	0.000	0.053
distGraph-class	0.000	0.000	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.016	0.000	0.017
edgeSets	0.028	0.000	0.030
edgeWeights	0.008	0.000	0.010
fromGXL-methods	0.532	0.020	0.571
graph-class	0.012	0.000	0.010
graph2SparseM	0.284	0.008	0.292
graphAM-class	0.016	0.004	0.016
graphBAM-class	0.068	0.000	0.068
graphExamples	0.004	0.000	0.005
graphNEL-class	0.004	0.000	0.006
inEdges	0.004	0.000	0.003
leaves	0.016	0.000	0.016
listEdges	0.012	0.000	0.015
matrix2Graph	0.032	0.000	0.030
mostEdges	0.020	0.000	0.024
numNoEdges	0.012	0.000	0.012
pancrCaIni	0.096	0.000	0.107
randomEGraph	0.012	0.000	0.013
randomGraph	0.008	0.000	0.009
randomNodeGraph	0.008	0.000	0.006
removeEdge	0.012	0.000	0.013
removeNode	0.004	0.000	0.004
renderInfo-class	0.012	0.000	0.013
reverseEdgeDirections	0.008	0.000	0.012
simpleEdge-class	0.000	0.000	0.002
standardLabeling	0.064	0.004	0.067
subGraph	0.004	0.000	0.002
toDotR-methods	0.040	0.004	0.047
ugraph	0.012	0.000	0.012
validGraph	0.004	0.000	0.002