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BioC 2.14: CHECK report for DEGraph on petty

This page was generated on 2014-10-08 08:59:17 -0700 (Wed, 08 Oct 2014).

Package 218/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGraph 1.16.0
Laurent Jacob
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/DEGraph
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DEGraph
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGraph_1.16.0.tar.gz
StartedAt: 2014-10-07 21:38:05 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:41:44 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 218.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DEGraph.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGraph_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/DEGraph.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGraph/DESCRIPTION’ ... OK
* this is package ‘DEGraph’ version ‘1.16.0’
* 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/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’ ‘KEGGgraph’ ‘lattice’ ‘RBGL’ ‘rrcov’ ‘Rgraphviz’ ‘NCIgraph’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘R.utils’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘graph:::getIndices’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [84s/85s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getKEGGPathways 14.174  0.049  14.320
plotValuedGraph 11.642  0.079  12.149
testOneGraph     8.193  0.056   8.346
AN.test          7.894  0.112   8.071
BS.test          7.293  0.066   7.400
hyper.test       7.266  0.058   7.493
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/DEGraph.Rcheck/00check.log’
for details.

DEGraph.Rcheck/00install.out:

* installing *source* package ‘DEGraph’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: 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
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (DEGraph)

DEGraph.Rcheck/DEGraph-Ex.timings:

nameusersystemelapsed
AN.test7.8940.1128.071
BS.test7.2930.0667.400
annLoi20080.3940.0130.412
classLoi20080.3750.0090.385
exprLoi20080.4080.0180.426
getConnectedComponentList3.8910.0153.912
getKEGGPathways14.174 0.04914.320
getSignedGraph3.7690.0153.804
grListKEGG2.3790.0222.491
graph.T2.test3.5140.0163.598
hyper.test7.2660.0587.493
laplacianFromA0.7640.0270.821
plotValuedGraph11.642 0.07912.149
randomWAMGraph0.7650.0250.820
testOneConnectedComponent3.6430.0133.695
testOneGraph8.1930.0568.346
twoSampleFromGraph0.7360.0260.783
writeAdjacencyMatrix2KGML0.7140.0250.792