BioC 3.2: CHECK report for marray on oaxaca

Package: marray

Version: 1.48.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings marray_1.48.0.tar.gz

StartedAt: 2016-04-23 01:42:50 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:43:56 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 65.2 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings marray_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/marray.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.48.0’
* 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 ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  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’
* 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 ... [22s/23s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
maNormMain 9.272  0.045   9.342
* 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-3.2-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	0.351	0.021	0.373
checkTargetInfo	0.077	0.006	0.082
dim	0.003	0.000	0.003
findID	0.077	0.005	0.082
htmlPage	0.126	0.007	0.134
image	0.068	0.004	0.073
ma2D	0.000	0.000	0.001
maBoxplot	0.001	0.000	0.001
maColorBar	0.014	0.002	0.016
maCompCoord	0.000	0.000	0.001
maCompInd	0.002	0.000	0.002
maCompLayout	0.005	0.000	0.006
maCompNormA	0	0	0
maCompPlate	0.007	0.001	0.007
maCoord2Ind	0.002	0.000	0.003
maDefaultPar	0.001	0.000	0.000
maDotsDefaults	0.003	0.001	0.003
maDotsMatch	0.002	0.001	0.003
maGenControls	0.190	0.003	0.193
maGeneTable	0.073	0.003	0.076
maImage	0.591	0.025	0.626
maImage.func	0.001	0.000	0.001
maInd2Coord	0.003	0.001	0.004
maLegendLines	0.001	0.000	0.001
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0.001	0.000	0.000
maMed	0.001	0.000	0.000
maNorm	1.449	0.018	1.473
maNorm2D	0.000	0.000	0.001
maNormLoess	0	0	0
maNormMAD	0.001	0.000	0.001
maNormMain	9.272	0.045	9.342
maNormMed	0.001	0.000	0.001
maNormScale	0.200	0.007	0.208
maNum2Logic	0.001	0.000	0.000
maPalette	0.024	0.001	0.027
maPlot	1.470	0.026	1.579
maPlot.func	0.000	0.000	0.001
maSelectGnames	0.010	0.001	0.010
maText	0	0	0
maTop	0.000	0.001	0.001
mapGeneInfo	0.001	0.000	0.002
marrayInfo-class	0.001	0.000	0.002
marrayLayout-class	0.001	0.000	0.002
marrayNorm-class	0.216	0.014	0.246
marrayRaw-class	0.116	0.009	0.126
opVersionID	0.002	0.001	0.002
plotMA	1.413	0.018	1.630
read.Galfile	0.112	0.000	0.112
read.marrayInfo	0.062	0.000	0.063
read.marrayLayout	0.178	0.002	0.180
read.marrayRaw	3.324	0.028	3.469
rm.na	0.001	0.000	0.001
stat.confband.text	0.582	0.020	0.603
stat.gnames	0.253	0.012	0.265
write.list	0.154	0.015	0.169
write.marray	0.075	0.003	0.079
write.xls	0.080	0.009	0.089