Package: graph

Version: 1.37.7

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.37.7.tar.gz

StartedAt: 2013-03-25 02:10:32 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:13:00 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 148.3 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/graph.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.37.7’
* 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 ... [9s/9s] OK
* checking installed package size ... OK
* checking package 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 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [8s/9s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [37s/38s]
 [38s/38s] 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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-2.12-bioc/meat/graph.Rcheck/graph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GraphClass.Rnw’ 
   ‘MultiGraphClass.Rnw’ 
   ‘clusterGraph.Rnw’ 
   ‘graph.Rnw’ 
   ‘graphAttributes.Rnw’ 
** testing if installed package can be loaded
* DONE (graph)

name	user	system	elapsed
DFS	0.064	0.004	0.068
IMCA	0.320	0.020	0.338
MAPKsig	0.248	0.020	0.268
MultiGraph-class	0.228	0.000	0.227
acc-methods	0.056	0.000	0.055
addEdge	0.048	0.000	0.049
addNode	0.060	0.000	0.059
adj-methods	0.032	0.000	0.033
apoptosisGraph	0.056	0.000	0.058
attrData-class	0.204	0.004	0.207
aveNumEdges	0.036	0.000	0.036
biocRepos	0.012	0.000	0.015
boundary	0.032	0.000	0.031
calcProb	0.020	0.000	0.021
calcSumProb	0.032	0.000	0.033
clearNode	0.044	0.000	0.042
clusterGraph-class	0.040	0.000	0.039
clusteringCoefficient-methods	0.044	0.000	0.043
combineNodes	0.092	0.004	0.097
distGraph-class	0.032	0.000	0.033
duplicatedEdges	0.012	0.000	0.013
edgeMatrix	0.064	0.000	0.066
edgeSets	0.288	0.004	0.292
edgeWeights	0.076	0.000	0.075
fromGXL-methods	0.624	0.012	0.636
graph-class	0.068	0.004	0.074
graph2SparseM	0.492	0.004	0.497
graphAM-class	0.268	0.000	0.265
graphBAM-class	0.168	0.004	0.173
graphExamples	0.028	0.000	0.027
graphNEL-class	0.040	0.000	0.042
inEdges	0.032	0.000	0.029
leaves	0.040	0.000	0.042
listEdges	0.040	0.000	0.039
matrix2Graph	0.116	0.000	0.116
mostEdges	0.072	0.000	0.071
numNoEdges	0.020	0.000	0.021
pancrCaIni	0.180	0.032	0.215
randomEGraph	0.028	0.004	0.032
randomGraph	0.036	0.004	0.041
randomNodeGraph	0.028	0.004	0.029
removeEdge	0.048	0.000	0.050
removeNode	0.032	0.000	0.034
renderInfo-class	0.052	0.008	0.060
reverseEdgeDirections	0.052	0.000	0.050
simpleEdge-class	0.024	0.004	0.030
standardLabeling	0.108	0.012	0.119
subGraph	0.048	0.000	0.047
toDotR-methods	0.08	0.00	0.08
ugraph	0.04	0.00	0.04
validGraph	0.032	0.000	0.028