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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BBCAnalyzer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BBCAnalyzer_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BBCAnalyzer.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BBCAnalyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BBCAnalyzer’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘BBCAnalyzer’ can be installed ... OK
* 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 code 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
analyzeBasesPlotOnly 17.176  0.415  17.656
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/BBCAnalyzer.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BBCAnalyzer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BBCAnalyzer’ ...
** using staged installation
** R
** 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 (BBCAnalyzer)