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This page was generated on 2021-10-15 15:06:41 -0400 (Fri, 15 Oct 2021).

CHECK results for marray on machv2

To the developers/maintainers of the marray package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/marray.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1033/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
marray 1.70.0  (landing page)
Yee Hwa (Jean) Yang
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/marray
git_branch: RELEASE_3_13
git_last_commit: 9f63605
git_last_commit_date: 2021-05-19 11:34:22 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: marray
Version: 1.70.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:marray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings marray_1.70.0.tar.gz
StartedAt: 2021-10-14 20:39:29 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:40:43 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 74.5 seconds
RetCode: 0
Status:   OK  
CheckDir: marray.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:marray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings marray_1.70.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/marray.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.70.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
maNormMain 9.732  0.102    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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/marray.Rcheck/00check.log’
for details.



Installation output

marray.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL marray
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output


Example timings

marray.Rcheck/marray-Ex.timings

nameusersystemelapsed
boxplot0.2990.0270.326
checkTargetInfo0.0750.0030.079
dim0.0020.0010.003
findID0.0970.0030.101
htmlPage0.0610.0030.064
image0.0790.0030.082
ma2D0.0000.0000.001
maBoxplot0.0000.0010.001
maColorBar0.0310.0030.034
maCompCoord0.0000.0010.002
maCompInd0.0020.0000.002
maCompLayout0.0060.0010.007
maCompNormA000
maCompPlate0.0030.0010.003
maCoord2Ind0.0010.0000.002
maDefaultPar000
maDotsDefaults0.0020.0000.002
maDotsMatch0.0020.0010.003
maGenControls0.2730.0040.277
maGeneTable0.0790.0030.082
maImage0.4390.0580.499
maImage.func0.0000.0000.001
maInd2Coord0.0020.0020.004
maLegendLines0.0000.0010.001
maLoess000
maLoessLines0.0010.0000.001
maMAD0.0000.0010.000
maMed000
maNorm1.3610.0221.383
maNorm2D000
maNormLoess000
maNormMAD000
maNormMain9.7320.1029.840
maNormMed000
maNormScale0.1330.0160.150
maNum2Logic000
maPalette0.2290.0050.235
maPlot2.3790.0912.475
maPlot.func0.0000.0000.001
maSelectGnames0.0060.0010.007
maText0.0000.0000.001
maTop0.0010.0010.000
mapGeneInfo0.0010.0010.001
marrayInfo-class0.0000.0010.001
marrayLayout-class0.0000.0010.001
marrayNorm-class0.3270.0180.347
marrayRaw-class0.0830.0080.091
opVersionID0.0020.0000.001
plotMA1.9320.0471.983
read.Galfile0.0500.0030.053
read.marrayInfo0.0240.0020.025
read.marrayLayout0.0520.0020.053
read.marrayRaw1.6420.0441.690
rm.na0.0000.0010.001
stat.confband.text0.4400.0100.451
stat.gnames0.2870.0110.298
write.list0.0880.0070.094
write.marray0.0740.0030.077
write.xls0.0710.0020.073