Package: marray

Version: 1.60.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:marray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings marray_1.60.0.tar.gz

StartedAt: 2019-04-16 01:00:04 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:01:08 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 64.7 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:marray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings marray_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/marray.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.60.0’
* 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  6.5Mb
  sub-directories of 1Mb or more:
    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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
maNormMain 9.671  0.167   9.964
* 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-3.8-bioc/meat/marray.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL marray
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘marray’ ...
** R
** data
** inst
** byte-compile and prepare 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	0.244	0.036	0.281
checkTargetInfo	0.082	0.006	0.088
dim	0.002	0.001	0.003
findID	0.076	0.005	0.082
htmlPage	0.088	0.014	0.101
image	0.069	0.003	0.072
ma2D	0	0	0
maBoxplot	0.000	0.000	0.001
maColorBar	0.068	0.005	0.074
maCompCoord	0.001	0.001	0.001
maCompInd	0.002	0.000	0.003
maCompLayout	0.005	0.001	0.005
maCompNormA	0	0	0
maCompPlate	0.003	0.000	0.003
maCoord2Ind	0.002	0.000	0.002
maDefaultPar	0	0	0
maDotsDefaults	0.002	0.001	0.003
maDotsMatch	0.002	0.001	0.002
maGenControls	0.242	0.006	0.247
maGeneTable	0.071	0.006	0.078
maImage	0.443	0.056	0.502
maImage.func	0	0	0
maInd2Coord	0.002	0.001	0.003
maLegendLines	0	0	0
maLoess	0.000	0.000	0.001
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0.001	0.000	0.000
maNorm	1.411	0.043	1.455
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0.001	0.000	0.000
maNormMain	9.671	0.167	9.964
maNormMed	0.000	0.000	0.001
maNormScale	0.127	0.019	0.163
maNum2Logic	0	0	0
maPalette	0.029	0.004	0.035
maPlot	1.590	0.049	1.647
maPlot.func	0	0	0
maSelectGnames	0.012	0.000	0.012
maText	0.000	0.000	0.001
maTop	0	0	0
mapGeneInfo	0.000	0.000	0.001
marrayInfo-class	0.000	0.001	0.000
marrayLayout-class	0.001	0.000	0.001
marrayNorm-class	0.165	0.026	0.191
marrayRaw-class	0.102	0.011	0.113
opVersionID	0.001	0.001	0.002
plotMA	1.452	0.026	1.486
read.Galfile	0.091	0.005	0.097
read.marrayInfo	0.044	0.001	0.045
read.marrayLayout	0.086	0.001	0.087
read.marrayRaw	2.067	0.028	2.099
rm.na	0.001	0.000	0.000
stat.confband.text	0.453	0.025	0.478
stat.gnames	0.287	0.022	0.309
write.list	0.097	0.013	0.110
write.marray	0.093	0.005	0.099
write.xls	0.087	0.014	0.100