Package: graph

Version: 1.34.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.34.0.tar.gz

StartedAt: 2012-09-24 01:25:34 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:26:57 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 83.3 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/graph.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.34.0’
* 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 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 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 ... NOTE
[.dist: warning in matrix(rval, nc = lenj, nr = leni): partial argument
  match of 'nr' to 'nrow'
[.dist: warning in matrix(rval, nc = lenj, nr = leni): partial argument
  match of 'nc' to 'ncol'
* 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 ... 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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/lib64 -o graph.so graph.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /loc/home/biocbuild/bbs-2.10-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	0.052	0.000	0.050
IMCA	0.448	0.020	0.471
MAPKsig	0.212	0.016	0.247
MultiGraph-class	0.104	0.004	0.113
acc-methods	0.020	0.000	0.023
addEdge	0.012	0.000	0.014
addNode	0.012	0.000	0.014
adj-methods	0.116	0.000	0.119
apoptosisGraph	0.024	0.008	0.033
attrData-class	0.000	0.000	0.001
aveNumEdges	0.012	0.000	0.012
biocRepos	0.000	0.004	0.002
boundary	0.004	0.000	0.011
buildRepDepGraph	0	0	0
calcProb	0.000	0.000	0.001
calcSumProb	0.012	0.000	0.011
clearNode	0.016	0.000	0.016
clusterGraph-class	0.004	0.000	0.004
clusteringCoefficient-methods	0.012	0.000	0.010
combineNodes	0.052	0.004	0.071
distGraph-class	0.000	0.000	0.006
duplicatedEdges	0	0	0
edgeMatrix	0.020	0.000	0.025
edgeSets	0.036	0.004	0.050
edgeWeights	0.016	0.000	0.014
fromGXL-methods	0.568	0.008	0.701
graph-class	0.012	0.000	0.010
graph2SparseM	0.172	0.008	0.209
graphAM-class	0.012	0.008	0.030
graphBAM-class	0.196	0.008	0.275
graphExamples	0.004	0.000	0.005
graphNEL-class	0.004	0.004	0.020
inEdges	0.008	0.000	0.006
leaves	0.012	0.000	0.016
listEdges	0.008	0.008	0.017
matrix2Graph	0.032	0.004	0.036
mostEdges	0.024	0.000	0.024
numNoEdges	0.008	0.004	0.011
pancrCaIni	0.088	0.000	0.097
randomEGraph	0.012	0.000	0.013
randomGraph	0.004	0.004	0.007
randomNodeGraph	0.004	0.000	0.005
removeEdge	0.012	0.000	0.011
removeNode	0.008	0.000	0.005
renderInfo-class	0.012	0.000	0.013
reverseEdgeDirections	0.012	0.000	0.012
simpleEdge-class	0.000	0.000	0.001
standardLabeling	0.060	0.004	0.063
subGraph	0.004	0.004	0.003
toDotR-methods	0.032	0.000	0.037
ugraph	0.012	0.000	0.009
validGraph	0.000	0.000	0.002