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BioC 2.12: CHECK report for DEGraph on george2

This page was generated on 2013-10-09 09:37:40 -0700 (Wed, 09 Oct 2013).

Package 173/671HostnameOS / ArchBUILDCHECKBUILD BIN
DEGraph 1.12.0
Laurent Jacob
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DEGraph
Last Changed Rev: 75263 / Revision: 81334
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 

Summary

Package: DEGraph
Version: 1.12.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DEGraph_1.12.0.tar.gz
StartedAt: 2013-10-09 01:17:24 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:21:30 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 246.4 seconds
RetCode: 0
Status:  OK 
CheckDir: DEGraph.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DEGraph.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.12.0’
* 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 ... [12s/12s] 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 ... [118s/120s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getKEGGPathways 37.838  0.136  38.543
plotValuedGraph 16.065  0.088  16.255
testOneGraph    13.973  0.036  14.088
AN.test          7.512  0.080   7.635
BS.test          7.209  0.072   7.289
hyper.test       6.065  0.072   6.340
getSignedGraph   5.273  0.024   5.303
* 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.test7.5120.0807.635
BS.test7.2090.0727.289
annLoi20080.3240.0040.327
classLoi20080.7240.0120.735
exprLoi20080.2600.0160.273
getConnectedComponentList4.3840.0244.410
getKEGGPathways37.838 0.13638.543
getSignedGraph5.2730.0245.303
grListKEGG1.9040.0321.940
graph.T2.test3.2680.0163.288
hyper.test6.0650.0726.340
laplacianFromA0.4800.0321.786
plotValuedGraph16.065 0.08816.255
randomWAMGraph0.7560.0240.815
testOneConnectedComponent3.5440.0123.641
testOneGraph13.973 0.03614.088
twoSampleFromGraph0.5560.0200.576
writeAdjacencyMatrix2KGML0.5240.0200.543