BioC 2.12: CHECK report for graph on george2

Package: graph

Version: 1.38.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.38.3.tar.gz

StartedAt: 2013-10-09 02:23:08 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:25:25 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 137.5 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 3.0.1 (2013-05-16)
* 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 ‘1.38.3’
* 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 ... [7s/8s] 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 ... [7s/8s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [36s/37s]
 [36s/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
** testing if installed package can be loaded
* DONE (graph)

name	user	system	elapsed
DFS	0.060	0.012	0.070
IMCA	0.328	0.000	0.332
MAPKsig	0.188	0.020	0.205
MultiGraph-class	0.220	0.008	0.228
acc-methods	0.040	0.000	0.041
addEdge	0.04	0.00	0.04
addNode	0.036	0.008	0.044
adj-methods	0.016	0.008	0.022
apoptosisGraph	0.044	0.004	0.047
attrData-class	0.048	0.000	0.049
aveNumEdges	0.024	0.008	0.030
biocRepos	0.008	0.008	0.015
boundary	0.02	0.00	0.02
calcProb	0.000	0.008	0.010
calcSumProb	0.032	0.000	0.034
clearNode	0.036	0.000	0.039
clusterGraph-class	0.028	0.004	0.045
clusteringCoefficient-methods	0.028	0.000	0.030
combineNodes	0.080	0.000	0.095
distGraph-class	0.028	0.004	0.038
duplicatedEdges	0.016	0.000	0.015
edgeMatrix	0.040	0.000	0.041
edgeSets	0.060	0.000	0.061
edgeWeights	0.180	0.000	0.363
fromGXL-methods	0.488	0.028	1.126
graph-class	0.072	0.004	0.152
graph2SparseM	0.408	0.004	0.492
graphAM-class	0.028	0.020	0.050
graphBAM-class	0.120	0.024	0.144
graphExamples	0.016	0.008	0.025
graphNEL-class	0.040	0.000	0.039
inEdges	0.020	0.000	0.021
leaves	0.028	0.004	0.033
listEdges	0.028	0.004	0.031
matrix2Graph	0.076	0.012	0.086
mostEdges	0.048	0.000	0.068
numNoEdges	0.032	0.000	0.058
pancrCaIni	0.184	0.004	0.186
randomEGraph	0.036	0.000	0.036
randomGraph	0.032	0.000	0.033
randomNodeGraph	0.024	0.000	0.025
removeEdge	0.048	0.000	0.047
removeNode	0.036	0.000	0.037
renderInfo-class	0.056	0.000	0.056
reverseEdgeDirections	0.044	0.000	0.041
simpleEdge-class	0.020	0.000	0.021
standardLabeling	0.14	0.00	0.14
subGraph	0.016	0.016	0.033
toDotR-methods	0.032	0.020	0.055
ugraph	0.024	0.000	0.025
validGraph	0.020	0.000	0.017