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BioC 2.12: CHECK report for DEGraph on petty

This page was generated on 2013-10-09 09:39:55 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGraph_1.12.0.tar.gz
StartedAt: 2013-10-08 22:09:27 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:13:29 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 242.7 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 3.0.1 (2013-05-16)
* 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 ... [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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [116s/117s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getKEGGPathways 30.661  0.186  31.208
plotValuedGraph 15.718  0.150  16.172
testOneGraph    13.498  0.105  13.708
AN.test          8.607  0.166   8.859
BS.test          8.112  0.095   8.344
hyper.test       7.785  0.176   8.033
getSignedGraph   5.079  0.037   5.139
* 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.test8.6070.1668.859
BS.test8.1120.0958.344
annLoi20080.5900.0180.608
classLoi20080.3940.0180.420
exprLoi20080.4110.0270.439
getConnectedComponentList4.5390.0374.627
getKEGGPathways30.661 0.18631.208
getSignedGraph5.0790.0375.139
grListKEGG2.8220.0812.915
graph.T2.test3.7750.0393.850
hyper.test7.7850.1768.033
laplacianFromA0.5870.0400.662
plotValuedGraph15.718 0.15016.172
randomWAMGraph0.6130.0380.675
testOneConnectedComponent3.8870.0503.996
testOneGraph13.498 0.10513.708
twoSampleFromGraph0.6780.0540.795
writeAdjacencyMatrix2KGML0.5990.0400.728