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Package 173/671HostnameOS / ArchBUILDCHECKBUILD BIN
DEGraph 1.12.0
Laurent Jacob
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DEGraph
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: DEGraph
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGraph_1.12.0.tar.gz
StartedAt: 2013-05-01 04:27:01 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 04:30:24 -0700 (Wed, 01 May 2013)
EllapsedTime: 203.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DEGraph.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DEGraph.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.12.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'DEGraph' can be installed ... [10s/11s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [93s/97s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getKEGGPathways 26.390  0.269  27.410
plotValuedGraph 12.081  0.184  12.747
testOneGraph     9.669  0.142   9.989
hyper.test       7.032  0.162   7.314
AN.test          6.907  0.171   7.226
BS.test          6.345  0.111   6.844
* 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

DEGraph.Rcheck/00install.out:

* installing *source* package 'DEGraph' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class
* DONE (DEGraph)

DEGraph.Rcheck/DEGraph-Ex.timings:

nameusersystemelapsed
AN.test6.9070.1717.226
BS.test6.3450.1116.844
annLoi20080.3220.0190.343
classLoi20080.3260.0190.346
exprLoi20080.3370.0370.373
getConnectedComponentList3.5030.0433.593
getKEGGPathways26.390 0.26927.410
getSignedGraph3.5830.0753.719
grListKEGG1.8710.0371.977
graph.T2.test3.0520.0533.164
hyper.test7.0320.1627.314
laplacianFromA0.4960.0450.578
plotValuedGraph12.081 0.18412.747
randomWAMGraph0.5370.0700.815
testOneConnectedComponent2.6480.0443.002
testOneGraph9.6690.1429.989
twoSampleFromGraph0.5560.0611.084
writeAdjacencyMatrix2KGML0.5030.0550.807