Package: graph

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.28.0.tar.gz

StartedAt: 2011-03-31 06:13:38 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:15:14 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 95.6 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/graph.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.28.0’
* 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 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 data for non-ASCII characters ... 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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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-2.7-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	0.090	0.000	0.092
IMCA	0.419	0.015	0.442
MAPKsig	0.238	0.021	0.425
MultiGraph-class	0.130	0.004	0.135
acc-methods	0.025	0.001	0.027
addEdge	0.021	0.001	0.022
addNode	0.019	0.000	0.019
adj-methods	0.012	0.000	0.012
apoptosisGraph	0.071	0.004	0.074
attrData-class	0.002	0.001	0.004
aveNumEdges	0.020	0.000	0.022
biocRepos	0.003	0.000	0.004
boundary	0.013	0.001	0.013
buildRepDepGraph	0.001	0.000	0.001
calcProb	0.000	0.000	0.001
calcSumProb	0.016	0.000	0.016
clearNode	0.012	0.001	0.012
clusterGraph-class	0.007	0.000	0.007
clusteringCoefficient-methods	0.020	0.001	0.021
combineNodes	0.075	0.000	0.076
distGraph-class	0.002	0.001	0.003
duplicatedEdges	0	0	0
edgeMatrix	0.026	0.001	0.027
edgeSets	0.057	0.002	0.063
edgeWeights	0.015	0.000	0.016
fromGXL-methods	0.709	0.018	0.751
graph-class	0.014	0.001	0.015
graph2SparseM	0.292	0.009	0.303
graphAM-class	0.092	0.000	0.093
graphBAM-class	0.094	0.002	0.102
graphExamples	0.011	0.001	0.013
graphNEL-class	0.010	0.001	0.011
inEdges	0.005	0.001	0.006
leaves	0.022	0.002	0.025
listEdges	0.018	0.001	0.019
matrix2Graph	0.042	0.002	0.044
mostEdges	0.037	0.001	0.039
numNoEdges	0.008	0.000	0.008
pancrCaIni	0.158	0.004	0.162
randomEGraph	0.017	0.001	0.017
randomGraph	0.012	0.000	0.012
randomNodeGraph	0.01	0.00	0.01
removeEdge	0.020	0.000	0.021
removeNode	0.007	0.000	0.008
renderInfo-class	0.019	0.001	0.019
reverseEdgeDirections	0.011	0.000	0.011
simpleEdge-class	0.002	0.000	0.002
standardLabeling	0.075	0.009	0.084
subGraph	0.003	0.000	0.003
toDotR-methods	0.046	0.006	0.052
ugraph	0.024	0.001	0.026
validGraph	0.004	0.000	0.004