Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-06 13:05:49 -0500 (Mon, 06 Dec 2021).

CHECK results for anota on machv2

To the developers/maintainers of the anota package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/anota.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 67/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anota 1.42.0  (landing page)
Ola Larsson
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/anota
git_branch: RELEASE_3_14
git_last_commit: 2ec6d93
git_last_commit_date: 2021-10-26 11:59:04 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: anota
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:anota.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings anota_1.42.0.tar.gz
StartedAt: 2021-12-05 11:46:11 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 11:48:04 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 113.2 seconds
RetCode: 0
Status:   OK  
CheckDir: anota.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:anota.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings anota_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/anota.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.42.0’
* 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 LazyData ... 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 21.331  0.218  21.582
* 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-3.14-bioc/meat/anota.Rcheck/00check.log’
for details.



Installation output

anota.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL anota
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
anotaDataSet0.0070.0050.012
anotaGetSigGenes000
anotaPerformQc000
anotaPlotSigGenes21.331 0.21821.582
anotaResidOutlierTest0.0010.0000.001