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CHECK report for arrayQuality on tokay1

This page was generated on 2018-04-12 13:17:29 -0400 (Thu, 12 Apr 2018).

Package 67/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayQuality 1.56.0
Agnes Paquet
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/arrayQuality
Branch: RELEASE_3_6
Last Commit: 3f98032
Last Changed Date: 2017-10-30 12:39:01 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: arrayQuality
Version: 1.56.0
Command: rm -rf arrayQuality.buildbin-libdir arrayQuality.Rcheck && mkdir arrayQuality.buildbin-libdir arrayQuality.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=arrayQuality.buildbin-libdir arrayQuality_1.56.0.tar.gz >arrayQuality.Rcheck\00install.out 2>&1 && cp arrayQuality.Rcheck\00install.out arrayQuality-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=arrayQuality.buildbin-libdir --install="check:arrayQuality-install.out" --force-multiarch --no-vignettes --timings arrayQuality_1.56.0.tar.gz
StartedAt: 2018-04-11 22:15:00 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:16:10 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 70.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: arrayQuality.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf arrayQuality.buildbin-libdir arrayQuality.Rcheck && mkdir arrayQuality.buildbin-libdir arrayQuality.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=arrayQuality.buildbin-libdir arrayQuality_1.56.0.tar.gz >arrayQuality.Rcheck\00install.out 2>&1 && cp arrayQuality.Rcheck\00install.out arrayQuality-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=arrayQuality.buildbin-libdir --install="check:arrayQuality-install.out" --force-multiarch --no-vignettes --timings arrayQuality_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/arrayQuality.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.56.0'
* 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/arrayQuality.Rcheck/00check.log'
for details.



Installation output

arrayQuality.Rcheck/00install.out


install for i386

* installing *source* package 'arrayQuality' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'arrayQuality'
    finding HTML links ... done
    MmDEGenes                               html  
    PRv9mers                                html  
    PRvQCHyb                                html  
    agQuality                               html  
    arrayQuality-internal                   html  
    globalQuality                           html  
    gpQuality                               html  
    gprDB                                   html  
    heeboQuality                            html  
    heeboQualityPlots                       html  
    maQualityPlots                          html  
    meeboQuality                            html  
    meeboQualityPlots                       html  
    prdata                                  html  
    qcScore                                 html  
    qualBoxplot                             html  
    qualityScore                            html  
    readAgilent                             html  
    readGPR                                 html  
    readSpikeTypes                          html  
    readSpot                                html  
    readcontrolCode                         html  
    scaleRefTable                           html  
    slideQuality                            html  
    spotQuality                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'arrayQuality' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'arrayQuality' as arrayQuality_1.56.0.zip
* DONE (arrayQuality)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

arrayQuality.Rcheck/examples_i386/arrayQuality-Ex.timings

nameusersystemelapsed
PRv9mers000
PRvQCHyb000
agQuality000
globalQuality000
gpQuality000
heeboQuality000
heeboQualityPlots000
maQualityPlots000
meeboQuality000
meeboQualityPlots000
qualBoxplot000
readGPR000
readSpikeTypes000
slideQuality000

arrayQuality.Rcheck/examples_x64/arrayQuality-Ex.timings

nameusersystemelapsed
PRv9mers000
PRvQCHyb000
agQuality000
globalQuality000
gpQuality000
heeboQuality000
heeboQualityPlots000
maQualityPlots000
meeboQuality000
meeboQualityPlots000
qualBoxplot000
readGPR000
readSpikeTypes000
slideQuality000