Package: graph

Version: 1.37.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.37.7.tar.gz

StartedAt: 2013-03-25 02:54:26 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:56:18 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 112.1 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/graph.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.37.7'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'graph' can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 installed files from 'inst/doc' ... OK
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'graph_unit_tests.R' [19s/19s]
 [20s/20s] 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 -DNDEBUG  -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-2.12-bioc/meat/graph.Rcheck/graph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GraphClass.Rnw' 
   'MultiGraphClass.Rnw' 
   'clusterGraph.Rnw' 
   'graph.Rnw' 
   'graphAttributes.Rnw' 
** testing if installed package can be loaded
* DONE (graph)

name	user	system	elapsed
DFS	0.049	0.009	0.058
IMCA	0.258	0.023	0.286
MAPKsig	0.170	0.017	0.189
MultiGraph-class	0.208	0.043	0.255
acc-methods	0.029	0.012	0.043
addEdge	0.025	0.012	0.037
addNode	0.029	0.015	0.046
adj-methods	0.021	0.010	0.031
apoptosisGraph	0.062	0.013	0.077
attrData-class	0.039	0.025	0.064
aveNumEdges	0.031	0.008	0.039
biocRepos	0.009	0.005	0.016
boundary	0.017	0.009	0.030
calcProb	0.008	0.005	0.014
calcSumProb	0.028	0.010	0.038
clearNode	0.023	0.010	0.035
clusterGraph-class	0.016	0.009	0.024
clusteringCoefficient-methods	0.019	0.007	0.027
combineNodes	0.058	0.014	0.073
distGraph-class	0.014	0.011	0.026
duplicatedEdges	0.007	0.006	0.014
edgeMatrix	0.029	0.011	0.041
edgeSets	0.063	0.009	0.073
edgeWeights	0.029	0.014	0.044
fromGXL-methods	0.452	0.046	0.500
graph-class	0.047	0.027	0.075
graph2SparseM	0.188	0.026	0.216
graphAM-class	0.043	0.017	0.065
graphBAM-class	0.162	0.038	0.204
graphExamples	0.013	0.007	0.020
graphNEL-class	0.020	0.015	0.037
inEdges	0.012	0.008	0.020
leaves	0.023	0.010	0.034
listEdges	0.022	0.011	0.033
matrix2Graph	0.051	0.016	0.068
mostEdges	0.050	0.009	0.064
numNoEdges	0.023	0.009	0.032
pancrCaIni	0.250	0.020	0.274
randomEGraph	0.023	0.008	0.030
randomGraph	0.020	0.008	0.028
randomNodeGraph	0.080	0.007	0.087
removeEdge	0.023	0.012	0.036
removeNode	0.013	0.009	0.023
renderInfo-class	0.024	0.013	0.037
reverseEdgeDirections	0.018	0.010	0.027
simpleEdge-class	0.006	0.005	0.011
standardLabeling	0.085	0.021	0.108
subGraph	0.023	0.012	0.035
toDotR-methods	0.065	0.018	0.084
ugraph	0.030	0.014	0.048
validGraph	0.020	0.009	0.028