Package: graph

Version: 1.31.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.31.1.tar.gz

StartedAt: 2011-05-09 15:05:04 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:06:40 -0700 (Mon, 09 May 2011)

EllapsedTime: 95.8 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/graph.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘1.31.1’
* 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 ... 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 sizes of PDF files under ‘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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c graph.c -o graph.o
gcc-4.2 -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-2.9-bioc/meat/graph.Rcheck/graph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘GraphClass.Rnw’ 
   ‘MultiGraphClass.Rnw’ 
   ‘clusterGraph.Rnw’ 
   ‘graph.Rnw’ 
   ‘graphAttributes.Rnw’ 
** testing if installed package can be loaded

* DONE (graph)

name	user	system	elapsed
DFS	0.109	0.001	0.110
IMCA	0.398	0.017	0.419
MAPKsig	0.221	0.012	0.247
MultiGraph-class	0.164	0.003	0.168
acc-methods	0.027	0.001	0.028
addEdge	0.021	0.000	0.021
addNode	0.018	0.000	0.019
adj-methods	0.01	0.00	0.01
apoptosisGraph	0.069	0.002	0.072
attrData-class	0.002	0.000	0.003
aveNumEdges	0.021	0.000	0.021
biocRepos	0.003	0.001	0.004
boundary	0.012	0.000	0.013
buildRepDepGraph	0.001	0.000	0.001
calcProb	0	0	0
calcSumProb	0.016	0.001	0.020
clearNode	0.015	0.001	0.016
clusterGraph-class	0.008	0.001	0.009
clusteringCoefficient-methods	0.020	0.000	0.021
combineNodes	0.084	0.001	0.085
distGraph-class	0.001	0.000	0.003
duplicatedEdges	0.000	0.000	0.001
edgeMatrix	0.032	0.001	0.034
edgeSets	0.062	0.004	0.068
edgeWeights	0.016	0.001	0.018
fromGXL-methods	0.824	0.019	0.864
graph-class	0.018	0.001	0.019
graph2SparseM	0.367	0.013	0.387
graphAM-class	0.021	0.001	0.021
graphBAM-class	0.092	0.001	0.094
graphExamples	0.009	0.001	0.010
graphNEL-class	0.008	0.000	0.009
inEdges	0.005	0.000	0.006
leaves	0.024	0.002	0.026
listEdges	0.017	0.001	0.019
matrix2Graph	0.048	0.002	0.049
mostEdges	0.038	0.001	0.039
numNoEdges	0.009	0.000	0.010
pancrCaIni	0.173	0.005	0.182
randomEGraph	0.015	0.000	0.015
randomGraph	0.015	0.000	0.015
randomNodeGraph	0.009	0.000	0.009
removeEdge	0.017	0.001	0.018
removeNode	0.007	0.000	0.008
renderInfo-class	0.021	0.000	0.022
reverseEdgeDirections	0.011	0.001	0.011
simpleEdge-class	0.002	0.000	0.002
standardLabeling	0.082	0.009	0.092
subGraph	0.003	0.001	0.003
toDotR-methods	0.055	0.006	0.063
ugraph	0.023	0.001	0.025
validGraph	0.004	0.000	0.004