BioC 3.4: CHECK report for EDASeq on morelia

Package: EDASeq

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EDASeq_2.8.0.tar.gz

StartedAt: 2017-04-15 01:24:56 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:29:12 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 255.3 seconds

RetCode: 0

Status:  OK

CheckDir: EDASeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EDASeq_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/EDASeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EDASeq/DESCRIPTION’ ... OK
* this is package ‘EDASeq’ version ‘2.8.0’
* 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 ‘EDASeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.availableOrgPkgs: no visible global function definition for
  ‘available.packages’
.gcLoess : ff: no visible global function definition for ‘quantile’
.gcLoess : ff: no visible global function definition for ‘loess’
.gcLoess : ff: no visible global function definition for ‘predict’
.gcLoess : ff: no visible global function definition for ‘median’
.gcQuant: no visible global function definition for ‘quantile’
.gcQuant : f : <anonymous>: no visible global function definition for
  ‘median’
.gcQuant : f : <anonymous>: no visible global function definition for
  ‘quantile’
.isAvailable: no visible global function definition for ‘biocLite’
newSeqExpressionSet: no visible global function definition for ‘new’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘smoothScatter’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘lines’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘lowess’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘abline’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘points’
MDPlot,matrix-numeric: no visible global function definition for
  ‘smoothScatter’
MDPlot,matrix-numeric: no visible global function definition for
  ‘lines’
MDPlot,matrix-numeric: no visible global function definition for
  ‘lowess’
MDPlot,matrix-numeric: no visible global function definition for
  ‘abline’
MDPlot,matrix-numeric: no visible global function definition for
  ‘points’
barplot,BamFileList: no visible global function definition for
  ‘countBam’
betweenLaneNormalization,matrix: no visible binding for global variable
  ‘quantile’
betweenLaneNormalization,matrix: no visible binding for global variable
  ‘median’
biasBoxplot,numeric-numeric: no visible global function definition for
  ‘quantile’
biasBoxplot,numeric-numeric: no visible global function definition for
  ‘abline’
biasPlot,matrix-numeric: no visible global function definition for
  ‘lowess’
biasPlot,matrix-numeric: no visible global function definition for
  ‘lines’
boxplot,FastqQuality: no visible global function definition for ‘as’
counts<-,SeqExpressionSet-ANY: no visible global function definition
  for ‘validObject’
exprs<-,SeqExpressionSet-ANY: no visible global function definition for
  ‘validObject’
initialize,SeqExpressionSet: no visible global function definition for
  ‘callNextMethod’
meanVarPlot,SeqExpressionSet: no visible binding for global variable
  ‘var’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘quantile’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘smoothScatter’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘lines’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘abline’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘lowess’
normCounts<-,SeqExpressionSet: no visible global function definition
  for ‘validObject’
offst<-,SeqExpressionSet: no visible global function definition for
  ‘validObject’
plot,BamFileList-FastqFileList: no visible global function definition
  for ‘elementMetadata’
plot,BamFileList-FastqFileList: no visible global function definition
  for ‘countBam’
plotNtFrequency,BamFile: no visible global function definition for
  ‘matplot’
plotNtFrequency,BamFile: no visible global function definition for
  ‘abline’
plotNtFrequency,BamFile: no visible global function definition for
  ‘legend’
plotNtFrequency,ShortRead: no visible global function definition for
  ‘matplot’
plotNtFrequency,ShortRead: no visible global function definition for
  ‘abline’
plotNtFrequency,ShortRead: no visible global function definition for
  ‘legend’
plotPCA,matrix: no visible global function definition for ‘text’
plotPCA,matrix: no visible global function definition for ‘pairs’
plotQuality,BamFile: no visible global function definition for
  ‘rainbow’
plotQuality,BamFile: no visible global function definition for ‘path’
plotQuality,BamFile: no visible global function definition for ‘narrow’
plotQuality,BamFile: no visible global function definition for ‘as’
plotQuality,BamFileList: no visible global function definition for
  ‘rainbow’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘path’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘narrow’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘as’
plotQuality,BamFileList: no visible global function definition for
  ‘lines’
plotQuality,FastqFileList: no visible global function definition for
  ‘rainbow’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘quality’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘path’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘narrow’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘as’
plotQuality,FastqFileList: no visible global function definition for
  ‘lines’
plotRLE,matrix: no visible global function definition for ‘abline’
updateObject,SeqExpressionSet: no visible global function definition
  for ‘callNextMethod’
Undefined global functions or variables:
  abline as available.packages biocLite callNextMethod countBam
  elementMetadata legend lines loess lowess matplot median narrow new
  pairs path points predict quality quantile rainbow smoothScatter text
  validObject var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "matplot", "pairs",
             "points", "smoothScatter", "text")
  importFrom("methods", "as", "callNextMethod", "new", "validObject")
  importFrom("stats", "loess", "lowess", "median", "predict", "quantile",
             "var")
  importFrom("utils", "available.packages")
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
Examples with CPU or elapsed time > 5s
                           user system elapsed
getGeneLengthAndGCContent 2.599  0.014   8.853
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘plotPCA.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/EDASeq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MDPlot-methods	0.549	0.018	2.838
SeqExpressionSet-class	0.073	0.003	0.115
betweenLaneNormalization-methods	0.082	0.005	0.169
biasBoxplot-methods	0.066	0.004	0.232
biasPlot-methods	0.163	0.010	1.375
getGeneLengthAndGCContent	2.599	0.014	8.853
newSeqExpressionSet	0.038	0.000	0.038
plotPCA-methods	0.845	0.028	0.887
plotRLE-methods	0.524	0.010	0.534
withinLaneNormalization-methods	0.179	0.007	0.186