Errors_Logs_And_Debugging Rnw to Rmd

[villafup]

@Bioconductor/sweave2rmd Initial conversion for review

Original Vignette

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• [x] the .Rmd file knits to HTML
• [ ] R CMD build runs without errors or timeouts
• [ ] the tarball from R CMD build contains the HTML (check with the following by substituting the package name and vignette name tar ztf package_name.tar.gz | grep 'doc/vignette_name')
• [ ] the .Rnw file has been removed
• In the DESCRIPTION file
  • [ ] BiocStyle and knitr are listed in Suggests
  • [ ] the line VignetteBuilder: knitr exists
  • [ ] any added lines use the same spacing and indents as the existing document
• If agreed with the Maintainer
  • [ ] the contributor is in the author list in the DESCRIPTION file*.
  • [ ] the contributor is in the author list in the vignette's YAML*.
• If this pull request involves converting from separate Author and Maintainer lines to the Authors@R vector, please ensure that
  • [ ] the Authors@R vector includes the maintainer as specified with role='cre'.
  • [ ] the Maintainer line is completely removed.
• [ ] HTML document is representative of the PDF in content and in general the presentation
• [ ] Where the contributor was not able to preserve the content and presentation of the PDF is noted as a comment in the pull request
• [ ] the R Markdown file is representative of the Sweave document and follows best practices, such as replacing links to Bioconductor packages with calls to BiocStyle's Biocpkg()
• [ ] Only files necessary for the conversion are included in the pull request.
• [ ] Long lines have been broken up and reformatted, you can achieve this by selecting the text in your script and then clicking on Code > Reflow Comment in R Studio.
• [ ] Code blocks are surrounded by a blank line, and there are no blank lines before the start or after the end of the code within the code block.