Package: DEGraph

Version: 1.10.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings DEGraph_1.10.0.tar.gz

StartedAt: 2013-03-25 00:37:26 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:40:24 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 178.2 seconds

RetCode: 0

Status:  OK

CheckDir: DEGraph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/DEGraph.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGraph/DESCRIPTION’ ... OK
* this is package ‘DEGraph’ version ‘1.10.0’
* 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 ‘DEGraph’ 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getKEGGPathways 27.233  0.132  28.031
plotValuedGraph 11.749  0.036  12.112
testOneGraph     9.809  0.280  10.430
AN.test          5.280  0.088   5.671
hyper.test       4.892  0.040   5.051
* 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
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘DEGraph.Rnw’ 
** testing if installed package can be loaded

* DONE (DEGraph)

name	user	system	elapsed
AN.test	5.280	0.088	5.671
BS.test	4.592	0.020	4.629
annLoi2008	0.192	0.004	0.195
classLoi2008	0.212	0.000	0.211
exprLoi2008	0.196	0.008	0.205
getConnectedComponentList	3.301	0.004	3.327
getKEGGPathways	27.233	0.132	28.031
getSignedGraph	3.420	0.000	3.439
grListKEGG	1.485	0.012	1.499
graph.T2.test	2.760	0.004	2.777
hyper.test	4.892	0.040	5.051
laplacianFromA	0.288	0.004	0.340
plotValuedGraph	11.749	0.036	12.112
randomWAMGraph	0.368	0.032	0.405
testOneConnectedComponent	2.488	0.012	2.504
testOneGraph	9.809	0.280	10.430
twoSampleFromGraph	0.292	0.008	0.328
writeAdjacencyMatrix2KGML	0.276	0.012	0.301