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BioC 3.0: CHECK report for DEGraph on perceval

This page was generated on 2015-04-10 09:55:25 -0700 (Fri, 10 Apr 2015).

Package 230/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGraph 1.18.0
Laurent Jacob
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DEGraph
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DEGraph
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGraph_1.18.0.tar.gz
StartedAt: 2015-04-10 00:40:46 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:43:11 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 144.5 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_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DEGraph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.18.0’
* 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 ... [9s/10s] 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getConnectedComponentList: no visible binding for global variable
  ‘Arguments’
getConnectedComponentList: no visible global function definition for
  ‘pushState’
getConnectedComponentList: no visible global function definition for
  ‘popState’
getKEGGPathways: no visible binding for global variable ‘Arguments’
getKEGGPathways: no visible global function definition for ‘pushState’
getKEGGPathways: no visible global function definition for ‘popState’
getKEGGPathways: no visible global function definition for
  ‘ProgressBar’
getKEGGPathways: no visible global function definition for ‘reset’
getKEGGPathways : <anonymous>: no visible global function definition
  for ‘increase’
getSignedGraph: no visible binding for global variable ‘Arguments’
getSignedGraph: no visible global function definition for ‘pushState’
getSignedGraph: no visible global function definition for ‘popState’
getSignedGraph: no visible global function definition for ‘enter’
getSignedGraph: no visible global function definition for ‘exit’
hyper.test: no visible binding for global variable ‘Arguments’
hyper.test: no visible global function definition for ‘pushState’
hyper.test: no visible global function definition for ‘popState’
plotValuedGraph: no visible binding for global variable ‘Arguments’
plotValuedGraph: no visible global function definition for ‘pushState’
plotValuedGraph: no visible global function definition for ‘popState’
randomWAMGraph: no visible binding for global variable ‘Arguments’
randomWAMGraph: no visible global function definition for ‘pushState’
randomWAMGraph: no visible global function definition for ‘popState’
testOneConnectedComponent: no visible binding for global variable
  ‘Arguments’
testOneConnectedComponent: no visible global function definition for
  ‘pushState’
testOneConnectedComponent: no visible global function definition for
  ‘popState’
testOneConnectedComponent: no visible global function definition for
  ‘enter’
testOneConnectedComponent: no visible global function definition for
  ‘exit’
testOneGraph: no visible binding for global variable ‘Arguments’
testOneGraph: no visible global function definition for ‘pushState’
testOneGraph: no visible global function definition for ‘popState’
testOneGraph: no visible global function definition for ‘enter’
testOneGraph: no visible global function definition for
  ‘translateNCI2GeneID’
testOneGraph: no visible global function definition for ‘exit’
writeAdjacencyMatrix2KGML: no visible binding for global variable
  ‘Arguments’
writeAdjacencyMatrix2KGML: no visible global function definition for
  ‘pushState’
writeAdjacencyMatrix2KGML: no visible global function definition for
  ‘popState’
* 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 ... [45s/49s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getKEGGPathways 6.651  0.044   6.784
plotValuedGraph 6.131  0.073   7.417
* 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
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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.test4.6490.0864.765
BS.test4.0930.0534.165
annLoi20080.2310.0130.243
classLoi20080.2170.0090.226
exprLoi20080.2520.0150.267
getConnectedComponentList2.1860.0162.209
getKEGGPathways6.6510.0446.784
getSignedGraph2.3060.0152.344
grListKEGG1.2190.0201.249
graph.T2.test1.4590.0121.472
hyper.test4.1630.0494.289
laplacianFromA0.3910.0220.721
plotValuedGraph6.1310.0737.417
randomWAMGraph0.3550.0191.166
testOneConnectedComponent1.3440.0051.352
testOneGraph4.3310.0574.423
twoSampleFromGraph0.3620.0230.915
writeAdjacencyMatrix2KGML0.3660.0251.175