Package: DEGraph

Version: 1.5.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch DEGraph_1.5.0.tar.gz

StartedAt: 2011-07-07 01:31:37 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:33:47 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 129.5 seconds

RetCode: 0

Status:  OK

CheckDir: DEGraph.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/DEGraph.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DEGraph' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 ... NOTE
testOneGraph: no visible global function definition for
  'translateNCI2GeneID'
* 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 examples ... 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 'DEGraph' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.8.0 (2011-04-03) successfully loaded. See ?R.oo for help.
R.utils v1.7.5 (2011-04-12) successfully loaded. See ?R.utils for help.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DEGraph.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (DEGraph)

name	user	system	elapsed
AN.test	4.78	0.04	4.92
BS.test	4.35	0.04	4.46
annLoi2008	0.22	0.00	0.41
classLoi2008	0.22	0.00	0.22
exprLoi2008	0.24	0.00	0.23
getConnectedComponentList	2.61	0.00	2.62
getKEGGPathways	20.00	0.01	23.05
getSignedGraph	3.02	0.00	3.08
grListKEGG	1.25	0.02	1.26
graph.T2.test	2.27	0.01	2.28
hyper.test	4.14	0.02	4.16
laplacianFromA	0.32	0.01	0.36
plotValuedGraph	9.64	0.05	9.75
randomWAMGraph	0.33	0.02	0.36
testOneConnectedComponent	2.42	0.01	2.45
testOneGraph	7.66	0.03	7.72
twoSampleFromGraph	0.29	0.03	0.35
writeAdjacencyMatrix2KGML	0.31	0.04	0.38