Package: marray

Version: 1.64.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:marray.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings marray_1.64.0.tar.gz

StartedAt: 2020-04-15 00:11:52 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:12:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 52.1 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:marray.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings marray_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/marray.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.64.0’
* 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  6.6Mb
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  length.na log.na mean.na prod.na quantile.na scale.na sum.na
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
maNormMain 7.528      0    7.55
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/marray.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL marray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘marray’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (marray)

name	user	system	elapsed
boxplot	0.156	0.012	0.170
checkTargetInfo	0.092	0.008	0.116
dim	0.000	0.000	0.002
findID	0.088	0.004	0.092
htmlPage	0.100	0.000	0.098
image	0.080	0.004	0.084
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.016	0.000	0.016
maCompCoord	0	0	0
maCompInd	0.004	0.000	0.001
maCompLayout	0.004	0.000	0.004
maCompNormA	0	0	0
maCompPlate	0.060	0.000	0.061
maCoord2Ind	0.004	0.000	0.003
maDefaultPar	0	0	0
maDotsDefaults	0.004	0.000	0.002
maDotsMatch	0.004	0.000	0.002
maGenControls	0.172	0.000	0.177
maGeneTable	0.084	0.000	0.087
maImage	0.420	0.028	0.464
maImage.func	0	0	0
maInd2Coord	0.000	0.004	0.002
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0.004	0.000	0.000
maMAD	0	0	0
maMed	0	0	0
maNorm	1.192	0.004	1.198
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	7.528	0.000	7.550
maNormMed	0	0	0
maNormScale	0.132	0.000	0.136
maNum2Logic	0	0	0
maPalette	0.024	0.000	0.026
maPlot	1.308	0.008	1.323
maPlot.func	0	0	0
maSelectGnames	0.004	0.000	0.003
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0.004	0.000	0.000
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.172	0.008	0.181
marrayRaw-class	0.060	0.012	0.070
opVersionID	0	0	0
plotMA	1.164	0.008	1.174
read.Galfile	0.056	0.004	0.367
read.marrayInfo	0.024	0.000	0.026
read.marrayLayout	0.060	0.000	0.058
read.marrayRaw	1.508	0.016	2.063
rm.na	0	0	0
stat.confband.text	0.252	0.000	0.252
stat.gnames	0.260	0.004	0.264
write.list	0.068	0.000	0.067
write.marray	0.060	0.000	0.057
write.xls	0.084	0.000	0.084