BioC 3.5: CHECK report for marray on tokay2

Package: marray

Version: 1.54.0

Command: rm -rf marray.buildbin-libdir marray.Rcheck && mkdir marray.buildbin-libdir marray.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=marray.buildbin-libdir marray_1.54.0.tar.gz >marray.Rcheck\00install.out 2>&1 && cp marray.Rcheck\00install.out marray-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=marray.buildbin-libdir --install="check:marray-install.out" --force-multiarch --no-vignettes --timings marray_1.54.0.tar.gz

StartedAt: 2017-10-18 01:03:08 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:04:46 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 98.4 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf marray.buildbin-libdir marray.Rcheck && mkdir marray.buildbin-libdir marray.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=marray.buildbin-libdir marray_1.54.0.tar.gz >marray.Rcheck\00install.out 2>&1 && cp marray.Rcheck\00install.out marray-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=marray.buildbin-libdir --install="check:marray-install.out" --force-multiarch --no-vignettes --timings marray_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/marray.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.54.0'
* 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 whether package 'marray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc         1.6Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
maNormMain 7.48      0    7.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
maNormMain 7.75   0.05     7.8
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/marray.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'marray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'marray' as marray_1.54.0.zip
* DONE (marray)

name	user	system	elapsed
boxplot	0.44	0.02	0.45
checkTargetInfo	0.14	0.00	0.14
dim	0.02	0.00	0.02
findID	0.09	0.00	0.09
htmlPage	0.16	0.00	0.16
image	0.07	0.01	0.09
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.04	0.00	0.03
maCompCoord	0	0	0
maCompInd	0.01	0.00	0.02
maCompLayout	0.05	0.00	0.04
maCompNormA	0	0	0
maCompPlate	0.01	0.00	0.02
maCoord2Ind	0	0	0
maDefaultPar	0	0	0
maDotsDefaults	0.02	0.00	0.01
maDotsMatch	0	0	0
maGenControls	0.12	0.02	0.14
maGeneTable	0.07	0.02	0.08
maImage	0.79	0.03	0.83
maImage.func	0	0	0
maInd2Coord	0	0	0
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	1.19	0.00	1.18
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	7.48	0.00	7.49
maNormMed	0	0	0
maNormScale	0.17	0.00	0.17
maNum2Logic	0	0	0
maPalette	0.03	0.00	0.03
maPlot	1.35	0.00	1.35
maPlot.func	0	0	0
maSelectGnames	0.01	0.00	0.01
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.21	0.01	0.22
marrayRaw-class	0.09	0.00	0.09
opVersionID	0	0	0
plotMA	1.16	0.00	1.16
read.Galfile	0.04	0.00	0.05
read.marrayInfo	0.05	0.00	0.04
read.marrayLayout	0.08	0.00	0.08
read.marrayRaw	1.98	0.02	2.00
rm.na	0	0	0
stat.confband.text	0.3	0.0	0.3
stat.gnames	0.17	0.00	0.17
write.list	0.11	0.00	0.11
write.marray	0.08	0.00	0.08
write.xls	0.09	0.00	0.09

name	user	system	elapsed
boxplot	0.46	0.00	0.47
checkTargetInfo	0.08	0.02	0.09
dim	0	0	0
findID	0.06	0.00	0.06
htmlPage	0.06	0.01	0.08
image	0.08	0.00	0.07
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.03	0.00	0.04
maCompCoord	0	0	0
maCompInd	0.02	0.00	0.01
maCompLayout	0.06	0.00	0.06
maCompNormA	0	0	0
maCompPlate	0	0	0
maCoord2Ind	0	0	0
maDefaultPar	0	0	0
maDotsDefaults	0	0	0
maDotsMatch	0	0	0
maGenControls	0.26	0.02	0.28
maGeneTable	0.10	0.00	0.09
maImage	0.92	0.00	0.93
maImage.func	0	0	0
maInd2Coord	0	0	0
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	1.26	0.03	1.29
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	7.75	0.05	7.80
maNormMed	0	0	0
maNormScale	0.24	0.01	0.25
maNum2Logic	0	0	0
maPalette	0.03	0.00	0.03
maPlot	1.61	0.05	1.66
maPlot.func	0	0	0
maSelectGnames	0.03	0.00	0.03
maText	0.02	0.00	0.01
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.18	0.02	0.21
marrayRaw-class	0.16	0.01	0.17
opVersionID	0	0	0
plotMA	1.19	0.00	1.19
read.Galfile	0.06	0.00	0.06
read.marrayInfo	0.06	0.00	0.06
read.marrayLayout	0.06	0.00	0.06
read.marrayRaw	2.53	0.02	2.55
rm.na	0	0	0
stat.confband.text	0.49	0.01	0.50
stat.gnames	0.23	0.03	0.26
write.list	0.14	0.00	0.14
write.marray	0.08	0.00	0.08
write.xls	0.08	0.00	0.08