Package: graph

Version: 1.29.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.29.3.tar.gz

StartedAt: 2011-03-17 16:33:29 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:34:33 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 64.8 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/graph.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.29.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
'library' or 'require' call not declared from: Rgraphviz
* 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'graph_unit_tests.R'
 OK
* checking package vignettes in 'inst/doc' ... 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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -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-2.8-bioc/meat/graph.Rcheck/graph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (graph)

name	user	system	elapsed
DFS	0.067	0.000	0.068
IMCA	0.258	0.006	0.265
MAPKsig	0.155	0.006	0.162
MultiGraph-class	0.102	0.002	0.104
acc-methods	0.017	0.000	0.018
addEdge	0.014	0.000	0.014
addNode	0.015	0.000	0.016
adj-methods	0.006	0.000	0.006
apoptosisGraph	0.051	0.002	0.053
attrData-class	0.002	0.001	0.002
aveNumEdges	0.015	0.000	0.014
biocRepos	0.004	0.000	0.004
boundary	0.009	0.000	0.010
buildRepDepGraph	0.000	0.001	0.000
calcProb	0	0	0
calcSumProb	0.009	0.000	0.010
clearNode	0.01	0.00	0.01
clusterGraph-class	0.004	0.000	0.005
clusteringCoefficient-methods	0.013	0.001	0.013
combineNodes	0.055	0.000	0.055
distGraph-class	0.001	0.000	0.001
duplicatedEdges	0	0	0
edgeMatrix	0.019	0.001	0.019
edgeSets	0.038	0.001	0.040
edgeWeights	0.012	0.000	0.012
fromGXL-methods	0.542	0.008	0.549
graph-class	0.010	0.001	0.011
graph2SparseM	0.249	0.004	0.253
graphAM-class	0.015	0.000	0.014
graphBAM-class	0.067	0.001	0.069
graphExamples	0.007	0.001	0.008
graphNEL-class	0.006	0.000	0.006
inEdges	0.004	0.000	0.004
leaves	0.018	0.001	0.018
listEdges	0.013	0.001	0.013
matrix2Graph	0.031	0.001	0.032
mostEdges	0.026	0.001	0.026
numNoEdges	0.006	0.000	0.006
pancrCaIni	0.112	0.002	0.114
randomEGraph	0.01	0.00	0.01
randomGraph	0.008	0.000	0.009
randomNodeGraph	0.008	0.000	0.008
removeEdge	0.012	0.000	0.012
removeNode	0.005	0.000	0.005
renderInfo-class	0.013	0.001	0.013
reverseEdgeDirections	0.008	0.000	0.007
simpleEdge-class	0.002	0.001	0.002
standardLabeling	0.059	0.003	0.062
subGraph	0.002	0.000	0.002
toDotR-methods	0.033	0.003	0.037
ugraph	0.014	0.001	0.014
validGraph	0.002	0.000	0.002