Package: graph

Version: 1.34.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.34.0.tar.gz

StartedAt: 2012-04-01 01:29:08 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:30:10 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 62.4 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/graph.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* 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/hpages/test-puck5/bbs-2.10-bioc/meat/graph.Rcheck/00check.log'
for details.

* installing *source* package 'graph' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/usr/local/lib -o graph.so graph.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /loc/home/hpages/test-puck5/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	0.032	0.000	0.035
IMCA	0.312	0.004	0.337
MAPKsig	0.132	0.004	0.171
MultiGraph-class	0.088	0.000	0.089
acc-methods	0.016	0.000	0.015
addEdge	0.056	0.000	0.057
addNode	0.008	0.000	0.010
adj-methods	0.004	0.000	0.005
apoptosisGraph	0.024	0.004	0.046
attrData-class	0.000	0.000	0.002
aveNumEdges	0.004	0.008	0.014
biocRepos	0.000	0.000	0.007
boundary	0.008	0.000	0.007
buildRepDepGraph	0	0	0
calcProb	0	0	0
calcSumProb	0.008	0.000	0.007
clearNode	0.012	0.000	0.009
clusterGraph-class	0.000	0.004	0.003
clusteringCoefficient-methods	0.008	0.000	0.009
combineNodes	0.040	0.000	0.039
distGraph-class	0.000	0.000	0.005
duplicatedEdges	0	0	0
edgeMatrix	0.012	0.000	0.013
edgeSets	0.036	0.000	0.046
edgeWeights	0.008	0.000	0.008
fromGXL-methods	0.376	0.004	0.402
graph-class	0.008	0.000	0.008
graph2SparseM	0.136	0.004	0.155
graphAM-class	0.016	0.000	0.016
graphBAM-class	0.104	0.000	0.106
graphExamples	0.004	0.000	0.009
graphNEL-class	0.000	0.004	0.005
inEdges	0.004	0.000	0.003
leaves	0.012	0.000	0.021
listEdges	0.008	0.004	0.011
matrix2Graph	0.028	0.000	0.025
mostEdges	0.020	0.004	0.024
numNoEdges	0.004	0.000	0.004
pancrCaIni	0.072	0.008	0.094
randomEGraph	0.008	0.000	0.008
randomGraph	0.008	0.000	0.007
randomNodeGraph	0.004	0.000	0.005
removeEdge	0.008	0.000	0.009
removeNode	0.004	0.000	0.003
renderInfo-class	0.012	0.000	0.011
reverseEdgeDirections	0.008	0.000	0.005
simpleEdge-class	0.000	0.000	0.001
standardLabeling	0.060	0.004	0.065
subGraph	0.004	0.000	0.009
toDotR-methods	0.024	0.000	0.027
ugraph	0.008	0.000	0.008
validGraph	0.004	0.000	0.002