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CHECK report for anota on tokay1

This page was generated on 2020-08-13 11:36:06 -0400 (Thu, 13 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 66/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anota 1.37.0
Ola Larsson
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:anota.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings anota_1.37.0.tar.gz
StartedAt: 2020-08-13 00:48:42 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 00:50:45 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 122.6 seconds
RetCode: 0
Status:  OK  
CheckDir: anota.Rcheck
Warnings: 0

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:anota.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings anota_1.37.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/anota.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
anotaPlotSigGenes 19.14   0.19   19.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
anotaPlotSigGenes 14.39   0.13   14.56
* 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: 3 NOTEs
See
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/anota_1.37.0.tar.gz && rm -rf anota.buildbin-libdir && mkdir anota.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=anota.buildbin-libdir anota_1.37.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL anota_1.37.0.zip && rm anota_1.37.0.tar.gz anota_1.37.0.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  418k  100  418k    0     0  4567k      0 --:--:-- --:--:-- --:--:-- 4751k

install for i386

* 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
  converting help for package 'anota'
    finding HTML links ... done
    anotaDataSet                            html  
    anotaGetSigGenes                        html  
    anotaPerformQc                          html  
    anotaPlotSigGenes                       html  
    anotaResidOutlierTest                   html  
** 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

install for x64

* installing *source* package 'anota' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'anota' as anota_1.37.0.zip
* DONE (anota)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'anota' successfully unpacked and MD5 sums checked

Tests output


Example timings

anota.Rcheck/examples_i386/anota-Ex.timings

nameusersystemelapsed
anotaDataSet0.020.000.02
anotaGetSigGenes000
anotaPerformQc000
anotaPlotSigGenes19.14 0.1919.92
anotaResidOutlierTest000

anota.Rcheck/examples_x64/anota-Ex.timings

nameusersystemelapsed
anotaDataSet0.010.000.02
anotaGetSigGenes000
anotaPerformQc000
anotaPlotSigGenes14.39 0.1314.56
anotaResidOutlierTest000