BioC 3.4: CHECK report for marray on morelia

Package: marray

Version: 1.52.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings marray_1.52.0.tar.gz

StartedAt: 2017-04-15 04:30:46 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 04:31:55 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 68.4 seconds

RetCode: 0

Status:  OK

CheckDir: marray.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 marray_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/marray.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 ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.52.0’
* 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 ‘marray’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc         1.5Mb
    swirldata   5.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
'library' or 'require' call to ‘tkWidgets’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
widget.marrayInfo : inputInfo: warning in assign(newname, newInfo, env
  = .GlobalEnv): partial argument match of 'env' to 'envir'
widget.marrayLayout : inputLayout: warning in assign(newname,
  newLayout, env = .GlobalEnv): partial argument match of 'env' to
  'envir'
widget.marrayRaw : inputRaw: warning in assign(newname, newRaw, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
addLines: no visible global function definition for ‘loess.control’
cor.na: no visible global function definition for ‘cor’
findID: no visible binding for global variable ‘gnames’
findID: no visible global function definition for ‘phenoData’
htmlPage: no visible binding for global variable ‘Gnames’
ma2D: no visible global function definition for ‘loess.control’
ma2D: no visible binding for global variable ‘na.omit’
ma2D: no visible global function definition for ‘loess’
ma2D: no visible global function definition for ‘predict’
maColorBar: no visible global function definition for ‘heat.colors’
maColorBar: no visible global function definition for ‘axis’
maColorBar: no visible global function definition for ‘par’
maColorBar: no visible global function definition for ‘box’
maCompNormA : <anonymous>: no visible global function definition for
  ‘ecdf’
maImage: no visible global function definition for ‘rainbow’
maImage: no visible global function definition for ‘layout’
maImage: no visible global function definition for ‘par’
maImage.func: no visible global function definition for ‘heat.colors’
maImage.func: no visible global function definition for ‘axis’
maImage.func: no visible global function definition for ‘contour’
maImage.func: no visible global function definition for ‘box’
maImage.func: no visible global function definition for ‘abline’
maLoess: no visible global function definition for ‘loess.control’
maLoess: no visible binding for global variable ‘na.omit’
maLoess: no visible global function definition for ‘loess’
maLoess: no visible global function definition for ‘predict’
maLoessLines: no visible global function definition for ‘loess.control’
maLoessLines : <anonymous>: no visible binding for global variable
  ‘loess’
maLoessLines : <anonymous>: no visible global function definition for
  ‘quantile’
maLoessLines : <anonymous>: no visible global function definition for
  ‘predict’
maLowessLines : <anonymous>: no visible global function definition for
  ‘lowess’
maMAD: no visible global function definition for ‘mad’
maMed: no visible global function definition for ‘median’
maPalette: no visible global function definition for ‘col2rgb’
maPalette: no visible global function definition for ‘rgb’
maPlot: no visible global function definition for ‘loess.control’
maPlot: no visible global function definition for ‘abline’
maTop: no visible global function definition for ‘quantile’
maTwoSamples: no visible global function definition for ‘gpTools’
quantile.na: no visible global function definition for ‘quantile’
read.Agilent: no visible binding for global variable ‘read.table’
read.Galfile: no visible binding for global variable ‘read.table’
read.marrayInfo: no visible global function definition for ‘read.table’
read.marrayRaw: no visible global function definition for ‘read.table’
scale.na: no visible global function definition for ‘applyy’
table2html: no visible global function definition for ‘browseURL’
var.na: no visible global function definition for ‘var’
widget.TwoSamples: no visible binding for global variable ‘fileBrowser’
widget.TwoSamples: no visible global function definition for
  ‘widgetRender’
widget.TwoSamples: no visible global function definition for
  ‘values.Widget’
widget.mapGeneInfo: no visible global function definition for
  ‘widgetRender’
widget.mapGeneInfo: no visible global function definition for
  ‘values.Widget’
widget.marrayInfo : inputInfo: no visible global function definition
  for ‘tclvalue’
widget.marrayInfo : fileBrow: no visible global function definition for
  ‘tkdelete’
widget.marrayInfo : fileBrow: no visible global function definition for
  ‘fileBrowser’
widget.marrayInfo : fileBrow: no visible global function definition for
  ‘tkinsert’
widget.marrayInfo: no visible global function definition for
  ‘tktoplevel’
widget.marrayInfo: no visible global function definition for
  ‘tkwm.title’
widget.marrayInfo: no visible global function definition for ‘tkframe’
widget.marrayInfo: no visible global function definition for ‘tkpack’
widget.marrayInfo: no visible global function definition for ‘tklabel’
widget.marrayInfo: no visible global function definition for ‘tkentry’
widget.marrayInfo: no visible global function definition for ‘tkbutton’
widget.marrayInfo: no visible global function definition for ‘tkgrid’
widget.marrayInfo: no visible global function definition for
  ‘tkgrid.configure’
widget.marrayInfo : <anonymous>: no visible global function definition
  for ‘tkdestroy’
widget.marrayLayout : inputLayout: no visible global function
  definition for ‘tclvalue’
widget.marrayLayout : listColnames: no visible global function
  definition for ‘tktoplevel’
widget.marrayLayout : listColnames: no visible global function
  definition for ‘tkwm.title’
widget.marrayLayout : listColnames: no visible global function
  definition for ‘tkframe’
widget.marrayLayout : listColnames: no visible global function
  definition for ‘tkpack’
widget.marrayLayout : listColnames: no visible global function
  definition for ‘tklabel’
widget.marrayLayout : listColnames: no visible global function
  definition for ‘tkcheckbutton’
widget.marrayLayout : listColnames : getResults: no visible global
  function definition for ‘tclvalue’
widget.marrayLayout : listColnames : getResults: no visible global
  function definition for ‘tkdestroy’
widget.marrayLayout : listColnames: no visible global function
  definition for ‘tkbutton’
widget.marrayLayout : fileBrow: no visible global function definition
  for ‘tkdelete’
widget.marrayLayout : fileBrow: no visible global function definition
  for ‘fileBrowser’
widget.marrayLayout : fileBrow: no visible global function definition
  for ‘tkinsert’
widget.marrayLayout: no visible global function definition for
  ‘tktoplevel’
widget.marrayLayout: no visible global function definition for
  ‘tkwm.title’
widget.marrayLayout: no visible global function definition for
  ‘tkframe’
widget.marrayLayout: no visible global function definition for ‘tkpack’
widget.marrayLayout: no visible global function definition for
  ‘tklabel’
widget.marrayLayout: no visible global function definition for
  ‘tkentry’
widget.marrayLayout: no visible global function definition for ‘tkgrid’
widget.marrayLayout: no visible global function definition for
  ‘tkgrid.configure’
widget.marrayLayout: no visible global function definition for
  ‘tkconfigure’
widget.marrayLayout: no visible global function definition for
  ‘tkbutton’
widget.marrayLayout : <anonymous>: no visible global function
  definition for ‘tclvalue’
widget.marrayLayout : <anonymous>: no visible global function
  definition for ‘tkdestroy’
widget.marrayRaw : inputRaw: no visible global function definition for
  ‘tclvalue’
widget.marrayRaw : filesClick: no visible global function definition
  for ‘fileBrowser’
widget.marrayRaw : browserToEntry: no visible global function
  definition for ‘objectBrowser’
widget.marrayRaw : browserToEntry: no visible global function
  definition for ‘tkdelete’
widget.marrayRaw : browserToEntry: no visible global function
  definition for ‘tkinsert’
widget.marrayRaw: no visible global function definition for
  ‘tktoplevel’
widget.marrayRaw: no visible global function definition for
  ‘tkwm.title’
widget.marrayRaw: no visible global function definition for ‘tkframe’
widget.marrayRaw: no visible global function definition for ‘tkpack’
widget.marrayRaw: no visible global function definition for ‘tkbutton’
widget.marrayRaw: no visible global function definition for ‘tklabel’
widget.marrayRaw: no visible global function definition for ‘tkentry’
widget.marrayRaw: no visible global function definition for ‘tkgrid’
widget.marrayRaw: no visible global function definition for
  ‘tkgrid.configure’
widget.marrayRaw : <anonymous>: no visible global function definition
  for ‘tkdestroy’
write.list: no visible global function definition for ‘write.table’
write.marray: no visible global function definition for ‘write.table’
write.xls: no visible binding for global variable ‘write.table’
show,ShowLargeObject: no visible global function definition for
  ‘printHead’
Undefined global functions or variables:
  Gnames abline applyy axis box browseURL col2rgb contour cor ecdf
  fileBrowser gnames gpTools heat.colors layout loess loess.control
  lowess mad median na.omit objectBrowser par phenoData predict
  printHead quantile rainbow read.table rgb tclvalue tkbutton
  tkcheckbutton tkconfigure tkdelete tkdestroy tkentry tkframe tkgrid
  tkgrid.configure tkinsert tklabel tkpack tktoplevel tkwm.title
  values.Widget var widgetRender write.table
Consider adding
  importFrom("grDevices", "col2rgb", "heat.colors", "rainbow", "rgb")
  importFrom("graphics", "abline", "axis", "box", "contour", "layout",
             "par")
  importFrom("stats", "cor", "ecdf", "loess", "loess.control", "lowess",
             "mad", "median", "na.omit", "predict", "quantile", "var")
  importFrom("utils", "browseURL", "read.table", "write.table")
to your NAMESPACE file.
* 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
maNormMain 8.515  0.044   8.568
* 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/marray.Rcheck/00check.log’
for details.

* installing *source* package ‘marray’ ...
** 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 (marray)

name	user	system	elapsed
boxplot	0.237	0.016	0.254
checkTargetInfo	0.062	0.005	0.067
dim	0.001	0.000	0.001
findID	0.055	0.003	0.059
htmlPage	0.062	0.006	0.067
image	0.075	0.004	0.079
ma2D	0.000	0.000	0.001
maBoxplot	0.000	0.000	0.001
maColorBar	0.010	0.001	0.011
maCompCoord	0.000	0.000	0.001
maCompInd	0.002	0.000	0.002
maCompLayout	0.005	0.001	0.005
maCompNormA	0.000	0.000	0.001
maCompPlate	0.007	0.000	0.007
maCoord2Ind	0.002	0.000	0.002
maDefaultPar	0.001	0.000	0.001
maDotsDefaults	0.002	0.000	0.003
maDotsMatch	0.002	0.001	0.003
maGenControls	0.197	0.005	0.202
maGeneTable	0.062	0.003	0.065
maImage	0.464	0.025	0.498
maImage.func	0	0	0
maInd2Coord	0.002	0.000	0.002
maLegendLines	0.001	0.000	0.000
maLoess	0.001	0.000	0.000
maLoessLines	0.001	0.000	0.000
maMAD	0.001	0.000	0.000
maMed	0	0	0
maNorm	1.106	0.006	1.114
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0.000	0.000	0.001
maNormMain	8.515	0.044	8.568
maNormMed	0	0	0
maNormScale	0.138	0.005	0.143
maNum2Logic	0.000	0.000	0.001
maPalette	0.020	0.001	0.023
maPlot	1.387	0.028	1.449
maPlot.func	0.000	0.001	0.001
maSelectGnames	0.007	0.000	0.008
maText	0.001	0.001	0.001
maTop	0.001	0.000	0.000
mapGeneInfo	0.001	0.000	0.001
marrayInfo-class	0	0	0
marrayLayout-class	0.001	0.000	0.001
marrayNorm-class	0.164	0.010	0.175
marrayRaw-class	0.117	0.010	0.131
opVersionID	0.002	0.000	0.001
plotMA	1.354	0.016	1.423
read.Galfile	0.100	0.001	0.101
read.marrayInfo	0.064	0.001	0.065
read.marrayLayout	0.131	0.003	0.133
read.marrayRaw	3.307	0.025	3.333
rm.na	0.001	0.000	0.002
stat.confband.text	0.421	0.018	0.455
stat.gnames	0.176	0.014	0.190
write.list	0.097	0.011	0.107
write.marray	0.054	0.004	0.058
write.xls	0.086	0.011	0.097