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CHECK report for yaqcaffy on tokay1

This page was generated on 2021-05-06 12:34:13 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the yaqcaffy package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1969/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
yaqcaffy 1.50.0  (landing page)
Laurent Gatto
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/yaqcaffy
Branch: RELEASE_3_12
Last Commit: b32e6b9
Last Changed Date: 2020-10-27 10:32:18 -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: yaqcaffy
Version: 1.50.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:yaqcaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings yaqcaffy_1.50.0.tar.gz
StartedAt: 2021-05-06 08:00:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:05:14 -0400 (Thu, 06 May 2021)
EllapsedTime: 283.1 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: yaqcaffy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:yaqcaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings yaqcaffy_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/yaqcaffy.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'yaqcaffy/DESCRIPTION' ... OK
* this is package 'yaqcaffy' version '1.50.0'
* 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 'yaqcaffy' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'simpleaffy' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/yaqcaffy.Rcheck/00install.out' for details.
* 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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getOutliers 23.20   1.47   25.03
getAllInt    9.11   0.70    9.81
getQCRatios  5.02   0.22    5.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getOutliers 27.19   0.92   28.11
getAllInt    9.62   0.23    9.86
getQCRatios  4.94   0.22    5.15
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/yaqcaffy.Rcheck/00check.log'
for details.



Installation output

yaqcaffy.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/yaqcaffy_1.50.0.tar.gz && rm -rf yaqcaffy.buildbin-libdir && mkdir yaqcaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=yaqcaffy.buildbin-libdir yaqcaffy_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL yaqcaffy_1.50.0.zip && rm yaqcaffy_1.50.0.tar.gz yaqcaffy_1.50.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 43123  100 43123    0     0  3214k      0 --:--:-- --:--:-- --:--:-- 3509k

install for i386

* installing *source* package 'yaqcaffy' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning message:
Package 'simpleaffy' is deprecated and will be removed from
  Bioconductor version 3.13 
Creating a generic function for 'identical' from package 'base' in package 'yaqcaffy'
** help
*** installing help indices
  converting help for package 'yaqcaffy'
    finding HTML links ... done
    YAQCStats-class                         html  
    finding level-2 HTML links ... done

    YaqcControlProbes-class                 html  
    getAllInt                               html  
    getBioProbes                            html  
    getOutliers                             html  
    getQCRatios                             html  
    getRatioProbes                          html  
    getSpikeProbes                          html  
    probeSelectionInterface                 html  
    reprodPlot                              html  
    yaqc.affy                               html  
    yaqc.plot                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'simpleaffy' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'simpleaffy' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'yaqcaffy' ...
** testing if installed package can be loaded
Warning: Package 'simpleaffy' is deprecated and will be removed from
  Bioconductor version 3.13
* MD5 sums
packaged installation of 'yaqcaffy' as yaqcaffy_1.50.0.zip
* DONE (yaqcaffy)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'yaqcaffy' successfully unpacked and MD5 sums checked

Tests output


Example timings

yaqcaffy.Rcheck/examples_i386/yaqcaffy-Ex.timings

nameusersystemelapsed
YaqcControlProbes-class000
getAllInt9.110.709.81
getBioProbes0.440.000.44
getOutliers23.20 1.4725.03
getQCRatios5.020.225.24
getRatioProbes0.500.010.52
getSpikeProbes0.550.030.58
probeSelectionInterface000
reprodPlot000
yaqc.affy3.970.074.03
yaqc.plot4.000.064.06

yaqcaffy.Rcheck/examples_x64/yaqcaffy-Ex.timings

nameusersystemelapsed
YaqcControlProbes-class000
getAllInt9.620.239.86
getBioProbes0.370.030.41
getOutliers27.19 0.9228.11
getQCRatios4.940.225.15
getRatioProbes0.460.020.49
getSpikeProbes0.540.010.54
probeSelectionInterface000
reprodPlot000
yaqc.affy3.950.184.13
yaqc.plot4.780.204.98