Package: graph

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.34.0.tar.gz

StartedAt: 2012-09-24 00:28:32 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:30:14 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 101.7 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/graph.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.34.0'
* 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 ... NOTE
[.dist: warning in matrix(rval, nc = lenj, nr = leni): partial argument
  match of 'nr' to 'nrow'
[.dist: warning in matrix(rval, nc = lenj, nr = leni): partial argument
  match of 'nc' to 'ncol'
* 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 ... 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/graph.Rcheck/00check.log'
for details.

* installing *source* package 'graph' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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-2.10-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	0.073	0.001	0.074
IMCA	0.594	0.028	0.624
MAPKsig	0.197	0.013	0.211
MultiGraph-class	0.217	0.007	0.225
acc-methods	0.029	0.001	0.030
addEdge	0.083	0.000	0.084
addNode	0.019	0.001	0.020
adj-methods	0.008	0.000	0.008
apoptosisGraph	0.069	0.005	0.074
attrData-class	0.002	0.001	0.003
aveNumEdges	0.023	0.003	0.026
biocRepos	0.003	0.001	0.006
boundary	0.015	0.000	0.016
buildRepDepGraph	0	0	0
calcProb	0	0	0
calcSumProb	0.013	0.000	0.014
clearNode	0.019	0.001	0.020
clusterGraph-class	0.007	0.000	0.008
clusteringCoefficient-methods	0.017	0.000	0.019
combineNodes	0.076	0.001	0.076
distGraph-class	0.001	0.000	0.002
duplicatedEdges	0	0	0
edgeMatrix	0.027	0.001	0.029
edgeSets	0.085	0.005	0.092
edgeWeights	0.014	0.000	0.015
fromGXL-methods	0.722	0.024	0.747
graph-class	0.014	0.001	0.015
graph2SparseM	0.271	0.016	0.289
graphAM-class	0.020	0.000	0.021
graphBAM-class	0.178	0.001	0.179
graphExamples	0.009	0.001	0.011
graphNEL-class	0.008	0.000	0.009
inEdges	0.005	0.000	0.005
leaves	0.020	0.002	0.022
listEdges	0.018	0.002	0.019
matrix2Graph	0.054	0.004	0.058
mostEdges	0.040	0.002	0.041
numNoEdges	0.008	0.000	0.008
pancrCaIni	0.163	0.008	0.170
randomEGraph	0.015	0.001	0.016
randomGraph	0.015	0.000	0.016
randomNodeGraph	0.008	0.000	0.009
removeEdge	0.017	0.000	0.017
removeNode	0.007	0.000	0.007
renderInfo-class	0.017	0.001	0.018
reverseEdgeDirections	0.012	0.001	0.012
simpleEdge-class	0.002	0.000	0.002
standardLabeling	0.099	0.010	0.109
subGraph	0.003	0.000	0.003
toDotR-methods	0.047	0.006	0.055
ugraph	0.015	0.001	0.015
validGraph	0.003	0.001	0.004