BioC 3.4: CHECK report for DEGraph on zin1

Package: DEGraph

Version: 1.25.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEGraph_1.25.1.tar.gz

StartedAt: 2016-09-20 05:26:56 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:27:58 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 62.2 seconds

RetCode: 0

Status:  OK

CheckDir: DEGraph.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEGraph_1.25.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DEGraph.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGraph/DESCRIPTION’ ... OK
* this is package ‘DEGraph’ version ‘1.25.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DEGraph’ can be installed ... 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
AN.test: no visible global function definition for ‘var’
BS.test: no visible global function definition for ‘pnorm’
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 ‘str’
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 ‘str’
getSignedGraph: no visible global function definition for ‘enter’
getSignedGraph: no visible global function definition for ‘exit’
getSignedGraph: no visible global function definition for ‘as’
graph.T2.test: no visible global function definition for ‘as’
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’
hyper.test: no visible global function definition for ‘str’
hyper.test: no visible global function definition for ‘phyper’
plotValuedGraph: no visible global function definition for
  ‘heat.colors’
plotValuedGraph: no visible binding for global variable ‘Arguments’
plotValuedGraph: no visible global function definition for ‘pushState’
plotValuedGraph: no visible global function definition for ‘popState’
plotValuedGraph: no visible global function definition for ‘str’
plotValuedGraph: no visible global function definition for ‘quantile’
randomWAMGraph: no visible binding for global variable ‘Arguments’
randomWAMGraph: no visible global function definition for ‘pushState’
randomWAMGraph: no visible global function definition for ‘popState’
randomWAMGraph: no visible global function definition for ‘as’
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’
testOneConnectedComponent: no visible global function definition for
  ‘as’
testOneConnectedComponent: no visible global function definition for
  ‘str’
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 ‘str’
testOneGraph: no visible global function definition for ‘exit’
twoSampleFromGraph: no visible global function definition for ‘rnorm’
writeAdjacencyMatrix2KGML: no visible binding for global variable
  ‘Arguments’
writeAdjacencyMatrix2KGML: no visible global function definition for
  ‘pushState’
writeAdjacencyMatrix2KGML: no visible global function definition for
  ‘popState’
writeAdjacencyMatrix2KGML : <anonymous>: no visible global function
  definition for ‘na.omit’
Undefined global functions or variables:
  Arguments ProgressBar as enter exit heat.colors increase na.omit
  phyper pnorm popState pushState quantile reset rnorm str
  translateNCI2GeneID var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("methods", "as")
  importFrom("stats", "na.omit", "phyper", "pnorm", "quantile", "rnorm",
             "var")
  importFrom("utils", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* 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

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/DEGraph.Rcheck/00check.log’
for details.

* installing *source* package ‘DEGraph’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEGraph)

name	user	system	elapsed
AN.test	2.208	0.028	2.248
BS.test	2.260	0.012	2.272
annLoi2008	0.168	0.000	0.164
classLoi2008	0.168	0.004	0.174
exprLoi2008	0.172	0.004	0.173
getConnectedComponentList	1.344	0.008	1.352
getKEGGPathways	3.840	0.000	3.902
getSignedGraph	1.468	0.000	1.469
grListKEGG	0.776	0.008	0.786
graph.T2.test	0.920	0.004	0.926
hyper.test	2.204	0.004	2.219
laplacianFromA	0.120	0.000	0.119
plotValuedGraph	2.996	0.008	3.015
randomWAMGraph	0.120	0.004	0.122
testOneConnectedComponent	0.952	0.004	0.955
testOneGraph	2.516	0.008	2.535
twoSampleFromGraph	0.124	0.000	0.124
writeAdjacencyMatrix2KGML	0.108	0.000	0.108