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CHECK report for anota on merida1

This page was generated on 2020-08-14 11:12:29 -0400 (Fri, 14 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE anota PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 66/1889HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anota 1.37.0
Ola Larsson
Snapshot Date: 2020-08-13 14:54:37 -0400 (Thu, 13 Aug 2020)
URL: https://git.bioconductor.org/packages/anota
Branch: master
Last Commit: e5ea588
Last Changed Date: 2020-04-27 14:25:34 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: anota
Version: 1.37.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:anota.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anota_1.37.0.tar.gz
StartedAt: 2020-08-13 23:18:48 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 23:20:47 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 119.1 seconds
RetCode: 0
Status:  OK 
CheckDir: anota.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:anota.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings anota_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/anota.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘anota/DESCRIPTION’ ... OK
* this is package ‘anota’ version ‘1.37.0’
* 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 ‘anota’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘qvalue’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘qvalue’
  All declared Imports should be used.
Package in Depends field not imported from: ‘qvalue’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
anotaAdjustPvalsQ: no visible global function definition for ‘qvalue’
anotaDfbsSummaryFull: no visible global function definition for ‘pdf’
anotaDfbsSummaryFull: no visible global function definition for
  ‘barplot’
anotaDfbsSummaryFull: no visible global function definition for
  ‘legend’
anotaDfbsSummaryFull: no visible global function definition for ‘text’
anotaDfbsSummaryFull: no visible global function definition for
  ‘dev.off’
anotaDfbsSummaryOnly: no visible global function definition for ‘lm’
anotaDfbsSummaryOnly: no visible global function definition for
  ‘dfbetas’
anotaGetSigGenes: no visible global function definition for
  ‘contrasts<-’
anotaGetSigGenes: no visible global function definition for
  ‘txtProgressBar’
anotaGetSigGenes: no visible global function definition for ‘lm’
anotaGetSigGenes: no visible global function definition for ‘anova’
anotaGetSigGenes: no visible global function definition for
  ‘setTxtProgressBar’
anotaGetSigGenes: no visible global function definition for ‘pf’
anotaGetSigGenes: no visible global function definition for ‘jpeg’
anotaGetSigGenes: no visible global function definition for ‘par’
anotaGetSigGenes: no visible global function definition for ‘dev.off’
anotaGetab : flik: no visible global function definition for ‘df’
anotaGetab: no visible global function definition for ‘nlm’
anotaPerformQc: no visible global function definition for ‘pdf’
anotaPerformQc: no visible global function definition for ‘par’
anotaPerformQc: no visible global function definition for
  ‘txtProgressBar’
anotaPerformQc: no visible global function definition for
  ‘setTxtProgressBar’
anotaPerformQc: no visible global function definition for ‘lm’
anotaPerformQc: no visible global function definition for ‘anova’
anotaPerformQc: no visible global function definition for ‘dfbetas’
anotaPerformQc: no visible global function definition for ‘dev.off’
anotaPerformQc: no visible global function definition for ‘jpeg’
anotaPerformRVM: no visible global function definition for ‘pf’
anotaPlotIGFit: no visible global function definition for ‘pf’
anotaPlotIGFit: no visible global function definition for ‘rf’
anotaPlotIGFit: no visible global function definition for ‘qqplot’
anotaPlotIGFit: no visible global function definition for ‘abline’
anotaPlotIGFit: no visible global function definition for ‘ks.test’
anotaPlotIGFit: no visible global function definition for ‘lines’
anotaPlotIGFit: no visible global function definition for ‘legend’
anotaPlotIntPvals: no visible global function definition for ‘pdf’
anotaPlotIntPvals: no visible global function definition for ‘par’
anotaPlotIntPvals: no visible global function definition for ‘density’
anotaPlotIntPvals: no visible global function definition for ‘hist’
anotaPlotIntPvals: no visible global function definition for ‘dev.off’
anotaPlotSigGenes: no visible global function definition for ‘pdf’
anotaPlotSigGenes: no visible global function definition for ‘par’
anotaPlotSigGenes: no visible global function definition for ‘text’
anotaPlotSigGenes: no visible global function definition for ‘lines’
anotaPlotSigGenes: no visible global function definition for ‘dev.off’
anotaPlotSingleRegression: no visible global function definition for
  ‘text’
anotaPlotSingleRegression: no visible global function definition for
  ‘lines’
anotaResidOutlierPlot: no visible global function definition for
  ‘matplot’
anotaResidOutlierPlot: no visible global function definition for ‘par’
anotaResidOutlierPlot: no visible global function definition for
  ‘segments’
anotaResidOutlierPlot: no visible global function definition for ‘axis’
anotaResidOutlierPlot: no visible global function definition for ‘box’
anotaResidOutlierPlot: no visible global function definition for
  ‘mtext’
anotaResidOutlierPlotAll: no visible global function definition for
  ‘points’
anotaResidOutlierPlotAll: no visible global function definition for
  ‘text’
anotaResidOutlierPlotAll: no visible global function definition for
  ‘segments’
anotaResidOutlierTest: no visible global function definition for ‘pdf’
anotaResidOutlierTest: no visible global function definition for ‘par’
anotaResidOutlierTest: no visible global function definition for
  ‘txtProgressBar’
anotaResidOutlierTest: no visible global function definition for
  ‘setTxtProgressBar’
anotaResidOutlierTest: no visible global function definition for
  ‘rnorm’
anotaResidOutlierTest: no visible global function definition for
  ‘qqnorm’
anotaResidOutlierTest: no visible global function definition for
  ‘dev.off’
anotaResidOutlierTest: no visible global function definition for ‘jpeg’
anotaSimDfbs: no visible global function definition for
  ‘txtProgressBar’
anotaSimDfbs: no visible global function definition for
  ‘setTxtProgressBar’
anotaSimDfbs: no visible global function definition for ‘rnorm’
anotaSimDfbs: no visible global function definition for ‘cor’
anotaSimDfbs: no visible global function definition for ‘median’
anotaSlopeTest: no visible global function definition for ‘pt’
getSummaryDfb: no visible binding for global variable ‘IQR’
Undefined global functions or variables:
  IQR abline anova axis barplot box contrasts<- cor density dev.off df
  dfbetas hist jpeg ks.test legend lines lm matplot median mtext nlm
  par pdf pf points pt qqnorm qqplot qvalue rf rnorm segments
  setTxtProgressBar text txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf")
  importFrom("graphics", "abline", "axis", "barplot", "box", "hist",
             "legend", "lines", "matplot", "mtext", "par", "points",
             "segments", "text")
  importFrom("stats", "IQR", "anova", "contrasts<-", "cor", "density",
             "df", "dfbetas", "ks.test", "lm", "median", "nlm", "pf",
             "pt", "qqnorm", "qqplot", "rf", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘anota.pdf’ from 558Kb to 428Kb
  consider running tools::compactPDF() on these files
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
anotaPlotSigGenes 21.189  0.317  22.066
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/anota.Rcheck/00check.log’
for details.



Installation output

anota.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL anota
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘anota’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (anota)

Tests output


Example timings

anota.Rcheck/anota-Ex.timings

nameusersystemelapsed
anotaDataSet0.0070.0040.011
anotaGetSigGenes000
anotaPerformQc000
anotaPlotSigGenes21.189 0.31722.066
anotaResidOutlierTest000