BioC 3.3: CHECK report for marray on linux2.bioconductor.org

Package: marray

Version: 1.49.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.49.0.tar.gz

StartedAt: 2015-10-27 05:25:50 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:26:43 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 52.4 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/marray.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.49.0’
* 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 ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  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
maImage: warning in layout(matrix(c(1, 2), 1, 2), width = c(8, 2)):
  partial argument match of 'width' to 'widths'
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'
findID: no visible binding for global variable ‘gnames’
findID: no visible global function definition for ‘phenoData’
htmlPage: no visible binding for global variable ‘Gnames’
maTwoSamples: no visible global function definition for ‘gpTools’
scale.na: no visible global function definition for ‘applyy’
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’
show,ShowLargeObject: no visible global function definition for
  ‘printHead’
Undefined global functions or variables:
  Gnames applyy fileBrowser gnames gpTools objectBrowser phenoData
  printHead tclvalue tkbutton tkcheckbutton tkconfigure tkdelete
  tkdestroy tkentry tkframe tkgrid tkgrid.configure tkinsert tklabel
  tkpack tktoplevel tkwm.title values.Widget widgetRender
* 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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
maNormMain 9.815  0.007    9.84
* 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
  ‘/home/biocbuild/bbs-3.3-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	0.349	0.005	0.353
checkTargetInfo	0.061	0.003	0.065
dim	0.002	0.001	0.002
findID	0.056	0.000	0.056
htmlPage	0.095	0.000	0.095
image	0.048	0.000	0.048
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.011	0.000	0.011
maCompCoord	0.001	0.000	0.001
maCompInd	0.002	0.000	0.002
maCompLayout	0.004	0.000	0.004
maCompNormA	0	0	0
maCompPlate	0.005	0.000	0.005
maCoord2Ind	0.002	0.000	0.002
maDefaultPar	0.001	0.000	0.001
maDotsDefaults	0.002	0.000	0.002
maDotsMatch	0.001	0.000	0.001
maGenControls	0.126	0.000	0.126
maGeneTable	0.083	0.000	0.083
maImage	0.436	0.007	0.444
maImage.func	0	0	0
maInd2Coord	0.001	0.000	0.001
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	1.27	0.00	1.27
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	9.815	0.007	9.840
maNormMed	0	0	0
maNormScale	0.133	0.004	0.137
maNum2Logic	0	0	0
maPalette	0.022	0.000	0.022
maPlot	1.665	0.004	1.670
maPlot.func	0.001	0.000	0.001
maSelectGnames	0.007	0.000	0.007
maText	0.001	0.000	0.001
maTop	0.001	0.000	0.001
mapGeneInfo	0.001	0.000	0.001
marrayInfo-class	0.001	0.000	0.001
marrayLayout-class	0.002	0.000	0.002
marrayNorm-class	0.267	0.008	0.275
marrayRaw-class	0.122	0.000	0.123
opVersionID	0.002	0.000	0.001
plotMA	1.850	0.008	1.862
read.Galfile	0.124	0.000	0.123
read.marrayInfo	0.047	0.000	0.047
read.marrayLayout	0.093	0.000	0.094
read.marrayRaw	2.139	0.012	2.150
rm.na	0.001	0.000	0.001
stat.confband.text	0.282	0.012	0.295
stat.gnames	0.226	0.000	0.227
write.list	0.077	0.000	0.077
write.marray	0.055	0.000	0.055
write.xls	0.060	0.000	0.061