Package: yaqcaffy

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings yaqcaffy_1.38.0.tar.gz

StartedAt: 2018-04-12 10:52:35 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:55:56 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 201.7 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings yaqcaffy_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yaqcaffy/DESCRIPTION’ ... OK
* this is package ‘yaqcaffy’ version ‘1.38.0’
* 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 ‘yaqcaffy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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:
  ‘MAQCsubsetAFX’ ‘tcltk’ ‘tcltk2’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘simpleaffy:::.bg.stats’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.isHgu133plus2: no visible global function definition for ‘cdfName’
.mergeAffyBatchObjects: no visible global function definition for
  ‘data’
.mergeAffyBatchObjects: no visible binding for global variable ‘refA’
.mergeAffyBatchObjects: no visible binding for global variable ‘refB’
.mergeAffyBatchObjects: no visible binding for global variable ‘refC’
.mergeAffyBatchObjects: no visible binding for global variable ‘refD’
.plotBioQC: no visible global function definition for ‘boxplot’
.plotBioQC: no visible global function definition for ‘text’
.plotBioQC: no visible global function definition for ‘sd’
.plotBioQC: no visible global function definition for ‘legend’
.plotSfs: no visible global function definition for ‘dotchart’
.plotSfs: no visible global function definition for ‘abline’
.plotSfs: no visible global function definition for ‘mtext’
.plotSfs: no visible global function definition for ‘sd’
.plotSpikesQC: no visible global function definition for ‘boxplot’
.plotSpikesQC: no visible global function definition for ‘text’
.plotSpikesQC: no visible global function definition for ‘sd’
.plotSpikesQC: no visible global function definition for ‘legend’
.plotdata: no visible global function definition for ‘boxplot’
.plotdata: no visible global function definition for ‘text’
.plotdata: no visible global function definition for ‘abline’
.plotdata: no visible global function definition for ‘qnorm’
.plotdata: no visible global function definition for ‘sd’
.plotdata: no visible global function definition for ‘mtext’
.plotdiag: no visible global function definition for ‘abline’
.plotrectangle: no visible global function definition for ‘sd’
.plotrectangle: no visible global function definition for ‘qnorm’
.plotrectangle: no visible global function definition for ‘rect’
.plotrectangle: no visible global function definition for ‘segments’
getBio: no visible global function definition for ‘featureNames’
getDeg: no visible global function definition for ‘cleancdfname’
getDeg: no visible global function definition for ‘cdfName’
getDeg: no visible global function definition for ‘featureNames’
getOutliers: no visible global function definition for ‘qnorm’
getOutliers: no visible global function definition for ‘sd’
getQcdefData: no visible global function definition for ‘cleancdfname’
getSpk: no visible global function definition for ‘featureNames’
probeSelectionInterface: no visible global function definition for
  ‘tkmessageBox’
probeSelectionInterface: no visible global function definition for
  ‘tktoplevel’
probeSelectionInterface: no visible global function definition for
  ‘tkframe’
probeSelectionInterface: no visible global function definition for
  ‘tkwm.title’
probeSelectionInterface: no visible global function definition for
  ‘tk2notebook’
probeSelectionInterface: no visible global function definition for
  ‘tkpack’
probeSelectionInterface: no visible global function definition for
  ‘tk2notetab’
probeSelectionInterface: no visible global function definition for
  ‘featureNames’
probeSelectionInterface: no visible global function definition for
  ‘tclVar’
probeSelectionInterface: no visible global function definition for
  ‘ttkcombobox’
probeSelectionInterface: no visible global function definition for
  ‘tklabel’
probeSelectionInterface: no visible global function definition for
  ‘tk2button’
probeSelectionInterface : <anonymous>: no visible global function
  definition for ‘tclvalue’
probeSelectionInterface : <anonymous>: no visible global function
  definition for ‘tkdestroy’
probeSelectionInterface: no visible global function definition for
  ‘tkgrid’
reprodPlot: no visible global function definition for ‘exprs’
reprodPlot: no visible global function definition for ‘gcrma’
reprodPlot: no visible global function definition for ‘mas5’
reprodPlot: no visible global function definition for ‘rma’
reprodPlot: no visible global function definition for ‘sampleNames’
reprodPlot: no visible global function definition for ‘par’
reprodPlot: no visible global function definition for ‘text’
reprodPlot: no visible global function definition for ‘smoothScatter’
reprodPlot: no visible global function definition for ‘mtext’
yaqc.affy.affybatch: no visible global function definition for
  ‘package.version’
yaqc.affy.affybatch: no visible global function definition for
  ‘experimentData’
yaqc.affy.affybatch : <anonymous>: no visible global function
  definition for ‘exprs’
yaqc.affy.affybatch: no visible global function definition for
  ‘sampleNames’
yaqc.affy.exprSet: no visible global function definition for
  ‘package.version’
yaqc.affy.exprSet : <anonymous>: no visible global function definition
  for ‘exprs’
yaqc.plot.all: no visible global function definition for ‘par’
yaqc.plot.all: no visible global function definition for ‘layout’
yaqc.plot.part: no visible global function definition for ‘layout’
yaqc.summary: no visible global function definition for ‘xtable’
Undefined global functions or variables:
  abline boxplot cdfName cleancdfname data dotchart experimentData
  exprs featureNames gcrma layout legend mas5 mtext package.version par
  qnorm rect refA refB refC refD rma sampleNames sd segments
  smoothScatter tclVar tclvalue text tk2button tk2notebook tk2notetab
  tkdestroy tkframe tkgrid tklabel tkmessageBox tkpack tktoplevel
  tkwm.title ttkcombobox xtable
Consider adding
  importFrom("graphics", "abline", "boxplot", "dotchart", "layout",
             "legend", "mtext", "par", "rect", "segments",
             "smoothScatter", "text")
  importFrom("stats", "qnorm", "sd")
  importFrom("utils", "data")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 25.779  0.949  27.286
getAllInt    9.573  0.350  10.198
yaqc.affy    5.916  0.386   6.449
getQCRatios  5.547  0.304   5.991
yaqc.plot    5.131  0.284   5.548
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/yaqcaffy.Rcheck/00check.log’
for details.

* installing *source* package ‘yaqcaffy’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘identical’ from package ‘base’ in package ‘yaqcaffy’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.003	0.001	0.004
getAllInt	9.573	0.350	10.198
getBioProbes	0.561	0.015	0.625
getOutliers	25.779	0.949	27.286
getQCRatios	5.547	0.304	5.991
getRatioProbes	0.676	0.018	0.707
getSpikeProbes	0.868	0.018	0.907
probeSelectionInterface	0.001	0.000	0.000
reprodPlot	0.001	0.000	0.001
yaqc.affy	5.916	0.386	6.449
yaqc.plot	5.131	0.284	5.548