Package: graph

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graph_1.30.0.tar.gz

StartedAt: 2011-10-20 15:23:02 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:24:36 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 93.8 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/graph.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.30.0'
* checking package namespace 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 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 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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-2.8-bioc/meat/graph.Rcheck/graph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (graph)

name	user	system	elapsed
DFS	0.065	0.000	0.066
IMCA	0.400	0.012	0.415
MAPKsig	0.234	0.011	0.288
MultiGraph-class	0.159	0.004	0.165
acc-methods	0.026	0.001	0.027
addEdge	0.019	0.000	0.019
addNode	0.020	0.001	0.020
adj-methods	0.009	0.001	0.010
apoptosisGraph	0.071	0.003	0.074
attrData-class	0.002	0.000	0.002
aveNumEdges	0.021	0.001	0.021
biocRepos	0.003	0.001	0.004
boundary	0.013	0.000	0.013
buildRepDepGraph	0.000	0.001	0.001
calcProb	0	0	0
calcSumProb	0.013	0.000	0.013
clearNode	0.013	0.000	0.013
clusterGraph-class	0.007	0.000	0.009
clusteringCoefficient-methods	0.018	0.001	0.018
combineNodes	0.074	0.001	0.085
distGraph-class	0.001	0.000	0.002
duplicatedEdges	0.001	0.000	0.000
edgeMatrix	0.029	0.001	0.030
edgeSets	0.057	0.004	0.060
edgeWeights	0.017	0.001	0.018
fromGXL-methods	0.703	0.014	0.734
graph-class	0.014	0.001	0.015
graph2SparseM	0.358	0.013	0.378
graphAM-class	0.021	0.000	0.021
graphBAM-class	0.113	0.002	0.115
graphExamples	0.010	0.001	0.011
graphNEL-class	0.009	0.001	0.009
inEdges	0.006	0.001	0.006
leaves	0.089	0.002	0.092
listEdges	0.019	0.001	0.020
matrix2Graph	0.054	0.005	0.062
mostEdges	0.040	0.002	0.043
numNoEdges	0.016	0.001	0.017
pancrCaIni	0.154	0.005	0.160
randomEGraph	0.015	0.000	0.015
randomGraph	0.011	0.000	0.012
randomNodeGraph	0.012	0.000	0.012
removeEdge	0.016	0.000	0.016
removeNode	0.007	0.000	0.007
renderInfo-class	0.017	0.001	0.017
reverseEdgeDirections	0.009	0.000	0.010
simpleEdge-class	0.002	0.000	0.002
standardLabeling	0.084	0.010	0.095
subGraph	0.002	0.000	0.003
toDotR-methods	0.049	0.005	0.063
ugraph	0.016	0.000	0.016
validGraph	0.007	0.000	0.008