Package: graph

Version: 1.35.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.35.1.tar.gz

StartedAt: 2012-06-21 00:42:17 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:44:02 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 104.9 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/graph.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'graph/DESCRIPTION' ... OK
* this is package 'graph' version '1.35.1'
* 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 ... 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 sizes of PDF files under 'inst/doc' ... 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

* installing *source* package 'graph' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c graph.c -o graph.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o graph.so graph.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mv graph.so BioC_graph.so
installing to /Users/biocbuild/bbs-2.11-bioc/meat/graph.Rcheck/graph/libs/i386
** 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	0.061	0.001	0.062
IMCA	0.546	0.025	0.590
MAPKsig	0.170	0.010	0.181
MultiGraph-class	0.198	0.006	0.206
acc-methods	0.022	0.001	0.024
addEdge	0.080	0.001	0.080
addNode	0.016	0.001	0.017
adj-methods	0.007	0.000	0.007
apoptosisGraph	0.062	0.003	0.070
attrData-class	0.002	0.000	0.002
aveNumEdges	0.020	0.003	0.023
biocRepos	0.002	0.001	0.004
boundary	0.011	0.001	0.012
calcProb	0	0	0
calcSumProb	0.011	0.001	0.011
clearNode	0.015	0.001	0.016
clusterGraph-class	0.006	0.000	0.006
clusteringCoefficient-methods	0.016	0.000	0.016
combineNodes	0.065	0.001	0.067
distGraph-class	0.002	0.000	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.023	0.001	0.025
edgeSets	0.070	0.004	0.075
edgeWeights	0.013	0.001	0.014
fromGXL-methods	0.635	0.019	0.702
graph-class	0.012	0.001	0.017
graph2SparseM	0.240	0.014	0.254
graphAM-class	0.028	0.001	0.028
graphBAM-class	0.150	0.002	0.156
graphExamples	0.008	0.001	0.010
graphNEL-class	0.007	0.001	0.007
inEdges	0.005	0.000	0.013
leaves	0.020	0.003	0.022
listEdges	0.017	0.002	0.019
matrix2Graph	0.041	0.002	0.043
mostEdges	0.041	0.001	0.042
numNoEdges	0.008	0.001	0.008
pancrCaIni	0.151	0.006	0.159
randomEGraph	0.013	0.001	0.015
randomGraph	0.011	0.000	0.013
randomNodeGraph	0.007	0.000	0.008
removeEdge	0.017	0.001	0.018
removeNode	0.006	0.001	0.008
renderInfo-class	0.019	0.001	0.021
reverseEdgeDirections	0.009	0.000	0.011
simpleEdge-class	0.002	0.000	0.002
standardLabeling	0.091	0.011	0.102
subGraph	0.003	0.000	0.003
toDotR-methods	0.043	0.005	0.052
ugraph	0.015	0.000	0.015
validGraph	0.003	0.000	0.004