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CHECK report for arrayQuality on merida1

This page was generated on 2021-05-06 12:34:20 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the arrayQuality package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 84/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayQuality 1.68.0  (landing page)
Agnes Paquet
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/arrayQuality
Branch: RELEASE_3_12
Last Commit: e40f17d
Last Changed Date: 2020-10-27 10:23:48 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: arrayQuality
Version: 1.68.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:arrayQuality.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings arrayQuality_1.68.0.tar.gz
StartedAt: 2021-05-05 23:16:53 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:17:48 -0400 (Wed, 05 May 2021)
EllapsedTime: 55.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: arrayQuality.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:arrayQuality.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings arrayQuality_1.68.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/arrayQuality.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘arrayQuality/DESCRIPTION’ ... OK
* this is package ‘arrayQuality’ version ‘1.68.0’
* 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 ‘arrayQuality’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 44.7Mb
  sub-directories of 1Mb or more:
    Heebo      17.1Mb
    Meebo      12.2Mb
    gprQCData  14.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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' calls in package code:
  ‘HEEBOdata’ ‘MEEBOdata’ ‘mclust’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PRv9mers: warning in layout(matrix(c(7, 1, 2, 7, 3, 3, 7, 4, 4, 7, 5,
  6), 3, 4), height = c(0.5, 4, 4), width = c(12, 5, 2, 7)): partial
  argument match of 'width' to 'widths'
PRv9mers: warning in layout(matrix(c(7, 1, 2, 7, 3, 3, 7, 4, 4, 7, 5,
  6), 3, 4), height = c(0.5, 4, 4), width = c(12, 5, 2, 7)): partial
  argument match of 'height' to 'heights'
PRvQCHyb: warning in layout(matrix(c(11, 1, 1, 2, 11, 3, 3, 7, 11, 4,
  4, 7, 11, 5, 5, 7, 11, 6, 6, 7, 11, 8, 9, 10), 4, 6), height = c(0.5,
  2, 2, 4), width = c(12, 5.5, 2, 5.5, 2, 7)): partial argument match
  of 'width' to 'widths'
PRvQCHyb: warning in layout(matrix(c(11, 1, 1, 2, 11, 3, 3, 7, 11, 4,
  4, 7, 11, 5, 5, 7, 11, 6, 6, 7, 11, 8, 9, 10), 4, 6), height = c(0.5,
  2, 2, 4), width = c(12, 5.5, 2, 5.5, 2, 7)): partial argument match
  of 'height' to 'heights'
PRvQCHyb: warning in qpDotPlots(mraw, x = "maA", col = colcode):
  partial argument match of 'x' to 'xvar'
PRvQCHyb: warning in qpDotPlots(mraw, x = "maA", col = colcode):
  partial argument match of 'col' to 'colcode'
heeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'width' to 'widths'
heeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'height' to 'heights'
heeboQualityPlots: warning in qpBoxplotMeebo(mraw, xvar = "maA", col =
  colcode, main = "Control A", cex.main = 0.8, id = controlId,
  meeboAnnot = HEEBOset): partial argument match of 'col' to 'colcode'
heeboQualityPlots: warning in qpDotPlotsEEBO(mraw, xvar = "maM", col =
  colcode, main = "Control M", cex.main = 0.8, id = seqId, meeboAnnot =
  HEEBOset): partial argument match of 'col' to 'colcode'
maQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'width' to 'widths'
maQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'height' to 'heights'
maQualityPlots: warning in qpDotPlots(mnorm, xvar = "maM", col =
  colcode, main = "Control normalized M", cex.main = 0.8, id =
  controlId): partial argument match of 'col' to 'colcode'
maQualityPlots: warning in qpDotPlots(mraw, xvar = "maA", col =
  colcode, main = "Control A", cex.main = 0.8, id = controlId): partial
  argument match of 'col' to 'colcode'
meeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'width' to 'widths'
meeboQualityPlots: warning in layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3,
  14, 4, 6, 6, 14, 5, 7, 7, 14, 8, 10, 11, 14, 9, 10, 11, 14, 12, 13,
  13), 4, 7), height = c(1, 10, 5, 5), width = c(11, 2, 5, 2, 5, 2,
  7)): partial argument match of 'height' to 'heights'
meeboQualityPlots: warning in qpBoxplotMeebo(mraw, xvar = "maA", col =
  colcode, main = "Control A", cex.main = 0.8, id = controlId,
  meeboAnnot = MEEBOset): partial argument match of 'col' to 'colcode'
meeboQualityPlots: warning in qpDotPlotsEEBO(mraw, xvar = "maM", col =
  colcode, main = "Control M", cex.main = 0.8, id = seqId, meeboAnnot =
  MEEBOset): partial argument match of 'col' to 'colcode'
qpBEplot.linear: warning in axis(1, at = seq(-50, 120, 10), label =
  seq(50, -120, -10)): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(1, at = seq(0, 90, 10), label = seq(0,
  90, 10)): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(1, at = c(-10, 100), label = c("WT",
  "Neg ctl")): partial argument match of 'label' to 'labels'
qpMisMatchPlot: warning in axis(4, at =
  quantile(mnorm$A[coreCollection, 1], c(0.25, 0.75, 0.9, 1), na.rm =
  TRUE), label = c(0.25, 0.75, 0.9, 1), las = 2): partial argument
  match of 'label' to 'labels'
qpTiling: warning in axis(1, at = unique(sort(-as.numeric(distance))),
  label = rev(unique(sort(as.numeric(distance))))): partial argument
  match of 'label' to 'labels'
EMSplit : meV.na: no visible global function definition for ‘me’
PRvQCHyb: no visible binding for global variable ‘MmDEGenes’
Spike.Cy5vsCy3: no visible binding for global variable ‘MEEBOset’
Spike.Cy5vsCy3: no visible binding for global variable ‘RG’
Spike.Individual.Sensitivity: no visible binding for global variable
  ‘RG’
Spike.Individual.Sensitivity: no visible binding for global variable
  ‘MEEBOset’
Spike.Individual.Sensitivity: no visible binding for global variable
  ‘MEEBOctrl’
Spike.MM.Scatter: no visible binding for global variable ‘RG’
Spike.MM.Scatter: no visible binding for global variable ‘MEEBOset’
Spike.MMplot: no visible binding for global variable ‘RG’
Spike.MMplot: no visible binding for global variable ‘MEEBOset’
Spike.Sensitivity: no visible binding for global variable ‘RG’
Spike.Sensitivity: no visible binding for global variable ‘MEEBOset’
arrayScal: no visible binding for global variable ‘MmReferenceDB’
getSpikeIds: no visible binding for global variable ‘MEEBOset’
getSpikeIndex: no visible binding for global variable ‘MEEBOset’
heeboQuality: no visible binding for global variable ‘HEEBOset’
heeboQuality: no visible binding for global variable ‘HEEBOctrl’
heeboQuality: no visible binding for global variable ‘HEEBOtilingres’
heeboQualityPlots: no visible binding for global variable ‘HEEBOset’
meeboQuality: no visible binding for global variable ‘MEEBOset’
meeboQuality: no visible binding for global variable ‘MEEBOctrl’
meeboQuality: no visible binding for global variable ‘MEEBOtilingres’
meeboQualityPlots: no visible binding for global variable ‘MEEBOset’
qpBEplot.linear: no visible binding for global variable ‘MEEBOctrl’
qpBoxplotMeebo: no visible binding for global variable ‘MEEBOset’
qpDotPlotsEEBO: no visible binding for global variable ‘MEEBOset’
qpDotPlotsMeebo: no visible binding for global variable ‘MEEBOset’
qpMisMatchPlot: no visible binding for global variable ‘HEEBOctrl’
qpTiling: no visible binding for global variable ‘MEEBOtilingres’
qualBoxplot: no visible binding for global variable ‘MmReferenceDB’
qualBoxplot: no visible binding for global variable ‘HsReferenceDB’
qualityScore: no visible binding for global variable ‘MmReferenceDB’
readAllSpikes: no visible binding for global variable ‘MEEBOset’
scaleRefTable: no visible binding for global variable ‘MmReferenceDB’
Undefined global functions or variables:
  HEEBOctrl HEEBOset HEEBOtilingres HsReferenceDB MEEBOctrl MEEBOset
  MEEBOtilingres MmDEGenes MmReferenceDB RG me
* checking Rd files ... NOTE
prepare_Rd: spotQuality.Rd:92-93: Dropping empty section \examples
* 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘basicQuality.html’, ‘customQuality.html’,
    ‘images/9mersDiagnosticPlot.png’, ‘images/QCHybDiagPlot.png’,
    ‘images/comparativeBoxplot.png’, ‘images/genHybDiagPlot.png’,
    ‘images/htmlReport.png’, ‘images/lifecycle.png’,
    ‘images/mySpotTypes.png’, ‘images/qualityDiagram.png’,
    ‘index.html’, ‘meeboQualityGuide.htm’,
    ‘meeboQualityGuide_files/filelist.xml’,
    ‘meeboQualityGuide_files/header.htm’,
    ‘meeboQualityGuide_files/image001.jpg’,
    ‘meeboQualityGuide_files/image003.jpg’,
    ‘meeboQualityGuide_files/image005.png’,
    ‘meeboQualityGuide_files/image007.png’,
    ‘meeboQualityGuide_files/image009.png’,
    ‘meeboQualityGuide_files/image011.png’,
    ‘meeboQualityGuide_files/image013.png’,
    ‘meeboQualityGuide_files/image015.png’,
    ‘meeboQualityGuide_files/image017.png’,
    ‘meeboQualityGuide_files/image019.png’,
    ‘meeboQualityGuide_files/image021.png’, ‘print-runQC.html’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/arrayQuality.Rcheck/00check.log’
for details.



Installation output

arrayQuality.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL arrayQuality
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘arrayQuality’ ...
** 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 (arrayQuality)

Tests output


Example timings

arrayQuality.Rcheck/arrayQuality-Ex.timings

nameusersystemelapsed
PRv9mers0.0010.0000.001
PRvQCHyb0.0010.0000.001
agQuality0.0030.0010.004
globalQuality0.0010.0000.001
gpQuality0.0010.0010.001
heeboQuality0.0010.0010.001
heeboQualityPlots0.0020.0010.002
maQualityPlots000
meeboQuality0.0000.0000.001
meeboQualityPlots0.0010.0010.001
qualBoxplot0.0010.0010.002
readGPR0.0000.0000.001
readSpikeTypes0.0010.0000.002
slideQuality0.0010.0000.002