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: 2011-07-07 03:40:22 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:42:02 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 100.0 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) (2011-06-22 r56208)
* 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 '1.31.1'
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                  old_size new_size compress
  esetsFemale.rda    121Kb     58Kb       xz
  esetsMale.rda      119Kb     56Kb       xz
* 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/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-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	0.067	0.001	0.067
IMCA	0.434	0.014	0.454
MAPKsig	0.240	0.012	0.290
MultiGraph-class	0.163	0.005	0.169
acc-methods	0.027	0.001	0.028
addEdge	0.019	0.000	0.020
addNode	0.020	0.000	0.021
adj-methods	0.009	0.001	0.009
apoptosisGraph	0.075	0.003	0.079
attrData-class	0.004	0.000	0.005
aveNumEdges	0.019	0.000	0.020
biocRepos	0.004	0.001	0.004
boundary	0.015	0.001	0.016
buildRepDepGraph	0	0	0
calcProb	0.000	0.000	0.001
calcSumProb	0.013	0.001	0.014
clearNode	0.013	0.001	0.014
clusterGraph-class	0.007	0.000	0.007
clusteringCoefficient-methods	0.018	0.000	0.018
combineNodes	0.075	0.001	0.076
distGraph-class	0.001	0.001	0.002
duplicatedEdges	0.001	0.000	0.000
edgeMatrix	0.028	0.001	0.029
edgeSets	0.059	0.003	0.062
edgeWeights	0.017	0.001	0.018
fromGXL-methods	0.724	0.016	0.765
graph-class	0.013	0.001	0.015
graph2SparseM	0.340	0.011	0.352
graphAM-class	0.027	0.000	0.028
graphBAM-class	0.144	0.002	0.151
graphExamples	0.011	0.001	0.011
graphNEL-class	0.010	0.001	0.011
inEdges	0.005	0.000	0.006
leaves	0.024	0.002	0.027
listEdges	0.019	0.002	0.020
matrix2Graph	0.045	0.002	0.047
mostEdges	0.038	0.002	0.040
numNoEdges	0.008	0.000	0.008
pancrCaIni	0.165	0.003	0.169
randomEGraph	0.015	0.000	0.016
randomGraph	0.014	0.001	0.014
randomNodeGraph	0.009	0.000	0.009
removeEdge	0.018	0.001	0.019
removeNode	0.007	0.000	0.007
renderInfo-class	0.021	0.000	0.024
reverseEdgeDirections	0.010	0.000	0.011
simpleEdge-class	0.001	0.000	0.002
standardLabeling	0.082	0.008	0.091
subGraph	0.002	0.001	0.003
toDotR-methods	0.050	0.006	0.057
ugraph	0.017	0.001	0.021
validGraph	0.008	0.000	0.008