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Package 170/658HostnameOS / ArchBUILDCHECKBUILD BIN
DEGraph 1.11.0
Laurent Jacob
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGraph
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
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 Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DEGraph
Version: 1.11.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DEGraph_1.11.0.tar.gz
StartedAt: 2013-03-25 01:06:59 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:11:09 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 250.0 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 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.11.0’
* 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 ... [121s/124s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getKEGGPathways 39.767  0.136  41.398
plotValuedGraph 16.157  0.060  16.722
testOneGraph    14.745  0.060  15.361
AN.test          7.976  0.080   8.208
BS.test          7.213  0.060   7.635
hyper.test       7.125  0.024   7.162
* 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
   ‘DEGraph.Rnw’ 
** 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.test7.9760.0808.208
BS.test7.2130.0607.635
annLoi20080.2880.0000.288
classLoi20080.3280.0080.340
exprLoi20080.7040.0240.728
getConnectedComponentList4.5120.0164.534
getKEGGPathways39.767 0.13641.398
getSignedGraph4.3040.0324.341
grListKEGG2.2520.0242.274
graph.T2.test3.8800.0163.897
hyper.test7.1250.0247.162
laplacianFromA0.4640.0080.472
plotValuedGraph16.157 0.06016.722
randomWAMGraph0.4920.0240.610
testOneConnectedComponent3.0680.0083.317
testOneGraph14.745 0.06015.361
twoSampleFromGraph0.6360.0160.650
writeAdjacencyMatrix2KGML0.5000.0160.513