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CHECK report for BBCAnalyzer on tokay2

This page was generated on 2021-01-24 12:32:15 -0500 (Sun, 24 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE BBCAnalyzer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 127/1932HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BBCAnalyzer 1.21.0
Sarah Sandmann
Snapshot Date: 2021-01-23 14:40:18 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/BBCAnalyzer
Branch: master
Last Commit: 24a6c8d
Last Changed Date: 2020-10-27 11:07:22 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BBCAnalyzer
Version: 1.21.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BBCAnalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.21.0.tar.gz
StartedAt: 2021-01-24 02:12:52 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 02:21:52 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 539.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BBCAnalyzer.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BBCAnalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BBCAnalyzer.Rcheck'
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BBCAnalyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BBCAnalyzer' version '1.21.0'
* 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 'BBCAnalyzer' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BBCAnalyzer.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analyzeBases: no visible global function definition for 'read.table'
analyzeBasesPlotOnly: no visible global function definition for
  'read.table'
analyzeReads: no visible global function definition for 'path'
analyzeReads: no visible global function definition for 'write.table'
checkBamInput: no visible global function definition for 'path'
checkVcfInput: no visible global function definition for 'path'
frequencyAnalysis: no visible global function definition for
  'write.table'
frequencyAnalysisVcf: no visible global function definition for
  'read.table'
frequencyAnalysisVcf: no visible global function definition for 'path'
frequencyAnalysisVcf: no visible global function definition for
  'write.table'
plotCountsPerSampleRelativeVcf_plot: no visible global function
  definition for 'par'
plotCountsPerSampleRelativeVcf_plot: no visible global function
  definition for 'barplot'
plotCountsPerSampleRelativeVcf_plot: no visible global function
  definition for 'rect'
plotCountsPerSampleRelativeVcf_plot: no visible global function
  definition for 'lines'
plotCountsPerSampleRelativeVcf_plot: no visible global function
  definition for 'text'
plotCountsPerSampleRelative_plot: no visible global function definition
  for 'par'
plotCountsPerSampleRelative_plot: no visible global function definition
  for 'barplot'
plotCountsPerSampleRelative_plot: no visible global function definition
  for 'rect'
plotCountsPerSampleRelative_plot: no visible global function definition
  for 'lines'
plotCountsPerSampleRelative_plot: no visible global function definition
  for 'text'
plotCountsPerSampleVcf_plot: no visible global function definition for
  'par'
plotCountsPerSampleVcf_plot: no visible global function definition for
  'barplot'
plotCountsPerSampleVcf_plot: no visible global function definition for
  'rect'
plotCountsPerSampleVcf_plot: no visible global function definition for
  'lines'
plotCountsPerSampleVcf_plot: no visible global function definition for
  'text'
plotCountsPerSample_plot: no visible global function definition for
  'par'
plotCountsPerSample_plot: no visible global function definition for
  'barplot'
plotCountsPerSample_plot: no visible global function definition for
  'rect'
plotCountsPerSample_plot: no visible global function definition for
  'lines'
plotCountsPerSample_plot: no visible global function definition for
  'text'
plotCountsPerTargetRelativeVcf_plot: no visible global function
  definition for 'par'
plotCountsPerTargetRelativeVcf_plot: no visible global function
  definition for 'barplot'
plotCountsPerTargetRelativeVcf_plot: no visible global function
  definition for 'rect'
plotCountsPerTargetRelativeVcf_plot: no visible global function
  definition for 'lines'
plotCountsPerTargetRelativeVcf_plot: no visible global function
  definition for 'text'
plotCountsPerTargetRelative_plot: no visible global function definition
  for 'par'
plotCountsPerTargetRelative_plot: no visible global function definition
  for 'barplot'
plotCountsPerTargetRelative_plot: no visible global function definition
  for 'rect'
plotCountsPerTargetRelative_plot: no visible global function definition
  for 'lines'
plotCountsPerTargetRelative_plot: no visible global function definition
  for 'text'
plotCountsPerTargetVcf_plot: no visible global function definition for
  'par'
plotCountsPerTargetVcf_plot: no visible global function definition for
  'barplot'
plotCountsPerTargetVcf_plot: no visible global function definition for
  'rect'
plotCountsPerTargetVcf_plot: no visible global function definition for
  'lines'
plotCountsPerTargetVcf_plot: no visible global function definition for
  'text'
plotCountsPerTarget_plot: no visible global function definition for
  'par'
plotCountsPerTarget_plot: no visible global function definition for
  'barplot'
plotCountsPerTarget_plot: no visible global function definition for
  'rect'
plotCountsPerTarget_plot: no visible global function definition for
  'lines'
plotCountsPerTarget_plot: no visible global function definition for
  'text'
processVcfFile: no visible global function definition for 'read.table'
reportVariants: no visible global function definition for 'write.table'
reportVariantsVcf: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  barplot lines par path read.table rect text write.table
Consider adding
  importFrom("graphics", "barplot", "lines", "par", "rect", "text")
  importFrom("utils", "read.table", "write.table")
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
analyzeBasesPlotOnly 32.24   0.81   33.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
analyzeBasesPlotOnly 27.99   0.23   28.22
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BBCAnalyzer.Rcheck/00check.log'
for details.



Installation output

BBCAnalyzer.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.13/bioc/src/contrib/BBCAnalyzer_1.21.0.tar.gz && rm -rf BBCAnalyzer.buildbin-libdir && mkdir BBCAnalyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BBCAnalyzer.buildbin-libdir BBCAnalyzer_1.21.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BBCAnalyzer_1.21.0.zip && rm BBCAnalyzer_1.21.0.tar.gz BBCAnalyzer_1.21.0.zip
###
##############################################################################
##############################################################################


  % 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 1798k  100 1798k    0     0  24.4M      0 --:--:-- --:--:-- --:--:-- 27.0M

install for i386

* installing *source* package 'BBCAnalyzer' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
** help
*** installing help indices
  converting help for package 'BBCAnalyzer'
    finding HTML links ... done
    BBCAnalyzer-package                     html  
REDIRECT:topic	 BBCAnalyzer -> BBCAnalyzer-package.html [ SUCCESS ]
REDIRECT:topic	 Bases By Cigar Analyzer -> BBCAnalyzer-package.html [ SUCCESS ]
REDIRECT:topic	 BasesByCigar Analyzer -> BBCAnalyzer-package.html [ SUCCESS ]
REDIRECT:topic	 BasesByCigarAnalyzer -> BBCAnalyzer-package.html [ SUCCESS ]
REDIRECT:topic	 Bases Coverage -> BBCAnalyzer-package.html [ SUCCESS ]
REDIRECT:topic	 Cigar Analysis -> BBCAnalyzer-package.html [ SUCCESS ]
REDIRECT:file	 BBCAnalyzer-package.html -> BBCAnalyzer-package.html [ SUCCESS ]
    analyzeBases                            html  
REDIRECT:topic	 analyzeBases -> analyzeBases.html [ SUCCESS ]
REDIRECT:topic	 analyze Bases -> analyzeBases.html [ SUCCESS ]
    analyzeBasesPlotOnly                    html  
REDIRECT:topic	 analyzeBasesPlotOnly -> analyzeBasesPlotOnly.html [ SUCCESS ]
REDIRECT:topic	 analyze Bases Plot Only -> analyzeBasesPlotOnly.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BBCAnalyzer' ...
** testing if installed package can be loaded
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer'
* MD5 sums
packaged installation of 'BBCAnalyzer' as BBCAnalyzer_1.21.0.zip
* DONE (BBCAnalyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BBCAnalyzer' successfully unpacked and MD5 sums checked

Tests output


Example timings

BBCAnalyzer.Rcheck/examples_i386/BBCAnalyzer-Ex.timings

nameusersystemelapsed
BBCAnalyzer-package0.180.060.25
analyzeBases0.210.050.25
analyzeBasesPlotOnly32.24 0.8133.17

BBCAnalyzer.Rcheck/examples_x64/BBCAnalyzer-Ex.timings

nameusersystemelapsed
BBCAnalyzer-package0.180.050.23
analyzeBases0.160.030.20
analyzeBasesPlotOnly27.99 0.2328.22