Package: yaqcaffy

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:yaqcaffy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings yaqcaffy_1.40.0.tar.gz

StartedAt: 2018-10-17 00:41:29 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:44:23 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 174.3 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:yaqcaffy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings yaqcaffy_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.40.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 18.183  0.860  19.048
getAllInt    5.669  0.262   5.935
* 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-3.7-bioc/meat/yaqcaffy.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL yaqcaffy
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘yaqcaffy’ ...
** R
** byte-compile and prepare 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	0.000	0.003
getAllInt	5.669	0.262	5.935
getBioProbes	0.375	0.012	0.387
getOutliers	18.183	0.860	19.048
getQCRatios	4.268	0.355	4.623
getRatioProbes	0.433	0.014	0.447
getSpikeProbes	0.514	0.011	0.525
probeSelectionInterface	0.001	0.000	0.001
reprodPlot	0.001	0.001	0.001
yaqc.affy	3.604	0.253	3.858
yaqc.plot	3.691	0.267	3.958