Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1168/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
marray 1.87.0  (landing page)
Yee Hwa (Jean) Yang
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/marray
git_branch: devel
git_last_commit: 4e46801
git_last_commit_date: 2025-04-15 09:34:26 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for marray on lconway

To the developers/maintainers of the marray package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: marray
Version: 1.87.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:marray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings marray_1.87.0.tar.gz
StartedAt: 2025-08-08 22:00:57 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 22:02:04 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 66.6 seconds
RetCode: 0
Status:   OK  
CheckDir: marray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:marray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings marray_1.87.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/marray.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.87.0’
* 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 ... OK
* checking installed package size ... INFO
  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 code 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
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 6.022  0.121   6.184
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/marray.Rcheck/00check.log’
for details.


Installation output

marray.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘marray’ ...
** this is package ‘marray’ version ‘1.87.0’
** 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
boxplot0.2020.0280.233
checkTargetInfo0.0520.0050.058
dim0.0010.0010.002
findID0.0520.0020.054
htmlPage0.0470.0040.051
image0.0390.0030.042
ma2D000
maBoxplot000
maColorBar0.0220.0030.026
maCompCoord0.0010.0010.001
maCompInd0.0020.0010.002
maCompLayout0.0040.0010.006
maCompNormA0.0000.0000.001
maCompPlate0.0030.0010.004
maCoord2Ind0.0020.0010.003
maDefaultPar0.0000.0010.000
maDotsDefaults0.0020.0010.004
maDotsMatch0.0020.0010.002
maGenControls0.1780.0040.183
maGeneTable0.0430.0020.046
maImage0.3230.0490.375
maImage.func000
maInd2Coord0.0010.0010.001
maLegendLines0.0010.0000.000
maLoess000
maLoessLines0.0000.0010.000
maMAD0.0000.0000.001
maMed0.0000.0000.001
maNorm0.8230.0360.868
maNorm2D000
maNormLoess000
maNormMAD000
maNormMain6.0220.1216.184
maNormMed0.0000.0010.000
maNormScale0.0860.0110.099
maNum2Logic000
maPalette0.1960.0050.203
maPlot1.7130.0851.827
maPlot.func0.0000.0000.001
maSelectGnames0.0030.0000.004
maText000
maTop0.0000.0000.001
mapGeneInfo0.0010.0010.001
marrayInfo-class000
marrayLayout-class0.0010.0000.000
marrayNorm-class0.2970.0180.317
marrayRaw-class0.0720.0230.095
opVersionID0.0010.0000.002
plotMA1.3810.0661.470
read.Galfile0.0490.0030.052
read.marrayInfo0.0220.0020.023
read.marrayLayout0.0470.0030.050
read.marrayRaw1.5570.0491.624
rm.na000
stat.confband.text0.3280.0190.353
stat.gnames0.1600.0110.171
write.list0.0560.0050.062
write.marray0.0630.0070.072
write.xls0.0470.0030.051