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This page was generated on 2023-01-28 11:06:17 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4510
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4288
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4317
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

CHECK results for arrayQuality on palomino4


To the developers/maintainers of the arrayQuality package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/arrayQuality.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 78/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayQuality 1.76.0  (landing page)
Agnes Paquet
Snapshot Date: 2023-01-27 14:00:04 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/arrayQuality
git_branch: RELEASE_3_16
git_last_commit: 7836fa3
git_last_commit_date: 2022-11-01 10:36:58 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: arrayQuality
Version: 1.76.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:arrayQuality.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings arrayQuality_1.76.0.tar.gz
StartedAt: 2023-01-27 22:58:26 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 22:59:14 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 48.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: arrayQuality.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:arrayQuality.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings arrayQuality_1.76.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/arrayQuality.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.76.0'
* 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 '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
  'F:/biocbuild/bbs-3.16-bioc/meat/arrayQuality.Rcheck/00check.log'
for details.



Installation output

arrayQuality.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL arrayQuality
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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
PRv9mers000
PRvQCHyb000
agQuality000
globalQuality000
gpQuality000
heeboQuality000
heeboQualityPlots000
maQualityPlots0.000.020.01
meeboQuality000
meeboQualityPlots000
qualBoxplot000
readGPR000
readSpikeTypes000
slideQuality000