Package: graph

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.32.0.tar.gz

StartedAt: 2012-03-24 01:43:39 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:45:13 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 93.7 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 2.14.2 (2012-02-29)
* 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 '1.32.0'
* 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 ... 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 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/Resources/include -I/Library/Frameworks/R.framework/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-2.9-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	0.096	0.001	0.097
IMCA	0.339	0.016	0.355
MAPKsig	0.219	0.012	0.237
MultiGraph-class	0.139	0.005	0.146
acc-methods	0.024	0.001	0.025
addEdge	0.015	0.000	0.016
addNode	0.022	0.001	0.022
adj-methods	0.007	0.000	0.008
apoptosisGraph	0.073	0.004	0.078
attrData-class	0.001	0.001	0.002
aveNumEdges	0.019	0.000	0.020
biocRepos	0.003	0.000	0.004
boundary	0.015	0.000	0.015
buildRepDepGraph	0.000	0.001	0.001
calcProb	0.000	0.000	0.001
calcSumProb	0.011	0.000	0.011
clearNode	0.011	0.000	0.012
clusterGraph-class	0.008	0.000	0.009
clusteringCoefficient-methods	0.014	0.001	0.015
combineNodes	0.116	0.003	0.120
distGraph-class	0.002	0.001	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.020	0.001	0.022
edgeSets	0.092	0.005	0.106
edgeWeights	0.015	0.000	0.015
fromGXL-methods	0.637	0.019	0.724
graph-class	0.011	0.001	0.014
graph2SparseM	0.344	0.013	0.360
graphAM-class	0.016	0.000	0.016
graphBAM-class	0.084	0.002	0.093
graphExamples	0.010	0.001	0.011
graphNEL-class	0.007	0.001	0.007
inEdges	0.005	0.001	0.005
leaves	0.019	0.002	0.022
listEdges	0.017	0.001	0.018
matrix2Graph	0.039	0.002	0.041
mostEdges	0.034	0.001	0.035
numNoEdges	0.014	0.000	0.014
pancrCaIni	0.231	0.008	0.241
randomEGraph	0.013	0.000	0.013
randomGraph	0.011	0.000	0.011
randomNodeGraph	0.009	0.001	0.010
removeEdge	0.015	0.001	0.015
removeNode	0.005	0.000	0.006
renderInfo-class	0.017	0.001	0.018
reverseEdgeDirections	0.008	0.001	0.008
simpleEdge-class	0.001	0.000	0.002
standardLabeling	0.084	0.009	0.095
subGraph	0.002	0.000	0.003
toDotR-methods	0.046	0.006	0.052
ugraph	0.014	0.001	0.015
validGraph	0.003	0.000	0.004