BioC 3.1: CHECK report for marray on petty

Package: marray

Version: 1.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings marray_1.46.0.tar.gz

StartedAt: 2015-10-09 00:02:41 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:04:48 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 126.9 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_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/marray.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.46.0’
* 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 ... [6s/11s] 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.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’
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’
show,ShowLargeObject: no visible global function definition for
  ‘printHead’
* 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 ... [36s/40s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
maNormMain 17.86   0.08  18.165
* 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-3.1-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	0.539	0.029	0.591
checkTargetInfo	0.116	0.006	0.123
dim	0.004	0.000	0.005
findID	0.108	0.006	0.114
htmlPage	0.206	0.014	0.219
image	0.158	0.008	0.166
ma2D	0.001	0.000	0.001
maBoxplot	0.001	0.000	0.001
maColorBar	0.022	0.002	0.045
maCompCoord	0.001	0.000	0.002
maCompInd	0.005	0.000	0.005
maCompLayout	0.010	0.001	0.011
maCompNormA	0.001	0.000	0.001
maCompPlate	0.009	0.000	0.010
maCoord2Ind	0.002	0.000	0.003
maDefaultPar	0.001	0.000	0.001
maDotsDefaults	0.004	0.001	0.025
maDotsMatch	0.002	0.001	0.003
maGenControls	0.325	0.005	0.337
maGeneTable	0.069	0.003	0.073
maImage	0.780	0.035	1.138
maImage.func	0.001	0.000	0.001
maInd2Coord	0.004	0.001	0.005
maLegendLines	0.001	0.000	0.001
maLoess	0.001	0.000	0.000
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0.000	0.000	0.001
maNorm	2.928	0.028	2.959
maNorm2D	0.001	0.000	0.001
maNormLoess	0.000	0.001	0.001
maNormMAD	0.000	0.000	0.001
maNormMain	17.860	0.080	18.165
maNormMed	0.001	0.000	0.001
maNormScale	0.275	0.011	0.291
maNum2Logic	0.000	0.000	0.001
maPalette	0.037	0.003	0.074
maPlot	2.818	0.055	3.742
maPlot.func	0.000	0.000	0.001
maSelectGnames	0.010	0.002	0.011
maText	0.001	0.000	0.002
maTop	0.000	0.001	0.001
mapGeneInfo	0.002	0.000	0.003
marrayInfo-class	0.002	0.000	0.001
marrayLayout-class	0.001	0.001	0.002
marrayNorm-class	0.335	0.015	0.396
marrayRaw-class	0.145	0.015	0.384
opVersionID	0.003	0.000	0.003
plotMA	2.601	0.035	2.965
read.Galfile	0.159	0.005	0.163
read.marrayInfo	0.165	0.002	0.167
read.marrayLayout	0.335	0.002	0.338
read.marrayRaw	2.912	0.032	2.949
rm.na	0.001	0.000	0.002
stat.confband.text	0.677	0.043	0.720
stat.gnames	0.340	0.018	0.369
write.list	0.149	0.015	0.173
write.marray	0.084	0.006	0.130
write.xls	0.204	0.020	0.225