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BioC 3.5: CHECK report for marray on tokay2

This page was generated on 2017-08-16 13:18:44 -0400 (Wed, 16 Aug 2017).

Package 752/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
marray 1.54.0
Yee Hwa (Jean) Yang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/marray
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: marray
Version: 1.54.0
Command: rm -rf marray.buildbin-libdir marray.Rcheck && mkdir marray.buildbin-libdir marray.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=marray.buildbin-libdir marray_1.54.0.tar.gz >marray.Rcheck\00install.out 2>&1 && cp marray.Rcheck\00install.out marray-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=marray.buildbin-libdir --install="check:marray-install.out" --force-multiarch --no-vignettes --timings marray_1.54.0.tar.gz
StartedAt: 2017-08-16 00:57:54 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:59:38 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 103.5 seconds
RetCode: 0
Status:  OK  
CheckDir: marray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf marray.buildbin-libdir marray.Rcheck && mkdir marray.buildbin-libdir marray.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=marray.buildbin-libdir marray_1.54.0.tar.gz >marray.Rcheck\00install.out 2>&1 && cp marray.Rcheck\00install.out marray-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=marray.buildbin-libdir --install="check:marray-install.out" --force-multiarch --no-vignettes --timings marray_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/marray.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.54.0'
* 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 whether package 'marray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc         1.6Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
maNormMain 8.28   0.04    8.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
maNormMain 7.65      0    7.66
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/marray.Rcheck/00check.log'
for details.


marray.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'marray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'marray' as marray_1.54.0.zip
* DONE (marray)

marray.Rcheck/examples_i386/marray-Ex.timings:

nameusersystemelapsed
boxplot0.460.000.45
checkTargetInfo0.090.000.10
dim000
findID0.070.000.08
htmlPage0.150.010.16
image0.070.000.08
ma2D000
maBoxplot000
maColorBar0.030.000.03
maCompCoord000
maCompInd0.020.000.02
maCompLayout0.040.000.05
maCompNormA000
maCompPlate0.020.000.01
maCoord2Ind000
maDefaultPar000
maDotsDefaults000
maDotsMatch000
maGenControls0.230.020.25
maGeneTable0.140.000.14
maImage1.000.011.02
maImage.func0.020.000.01
maInd2Coord000
maLegendLines000
maLoess000
maLoessLines000
maMAD000
maMed000
maNorm1.220.001.22
maNorm2D000
maNormLoess000
maNormMAD000
maNormMain8.280.048.31
maNormMed000
maNormScale0.210.000.20
maNum2Logic000
maPalette0.030.000.03
maPlot1.50.01.5
maPlot.func000
maSelectGnames0.010.000.02
maText000
maTop000
mapGeneInfo000
marrayInfo-class000
marrayLayout-class000
marrayNorm-class0.190.010.20
marrayRaw-class0.140.000.14
opVersionID000
plotMA1.190.001.19
read.Galfile0.040.020.06
read.marrayInfo0.050.000.05
read.marrayLayout0.080.000.07
read.marrayRaw2.670.082.75
rm.na000
stat.confband.text0.360.000.36
stat.gnames0.190.000.19
write.list0.140.000.14
write.marray0.080.000.08
write.xls0.070.010.09

marray.Rcheck/examples_x64/marray-Ex.timings:

nameusersystemelapsed
boxplot0.490.030.51
checkTargetInfo0.090.000.10
dim000
findID0.080.000.08
htmlPage0.090.000.10
image0.090.000.09
ma2D000
maBoxplot000
maColorBar0.050.000.05
maCompCoord000
maCompInd0.020.000.01
maCompLayout0.070.000.08
maCompNormA000
maCompPlate0.020.000.02
maCoord2Ind000
maDefaultPar000
maDotsDefaults0.010.000.01
maDotsMatch000
maGenControls0.150.000.14
maGeneTable0.070.000.08
maImage0.860.000.86
maImage.func000
maInd2Coord000
maLegendLines000
maLoess000
maLoessLines000
maMAD000
maMed000
maNorm1.470.001.46
maNorm2D000
maNormLoess000
maNormMAD000
maNormMain7.650.007.66
maNormMed000
maNormScale0.130.000.13
maNum2Logic000
maPalette0.010.000.01
maPlot1.690.001.69
maPlot.func000
maSelectGnames0.030.000.03
maText000
maTop000
mapGeneInfo000
marrayInfo-class000
marrayLayout-class000
marrayNorm-class0.270.010.28
marrayRaw-class0.110.000.11
opVersionID000
plotMA1.330.001.33
read.Galfile0.060.000.07
read.marrayInfo0.110.000.11
read.marrayLayout0.100.000.09
read.marrayRaw2.360.022.37
rm.na000
stat.confband.text0.400.000.41
stat.gnames0.190.000.19
write.list0.110.000.10
write.marray0.060.000.07
write.xls0.080.010.09