Errors_Logs_And_Debugging Rnw to Rmd

[villafup]

@Bioconductor/sweave2rmd Initial conversion for review

Original Vignette

[jwokaty]

Hi @villafup, we just need a few changes before this is ready for the maintainers to review. Please do the following:

• Remove .Rnw
• Modify the author section in the .Rmd to include yourself as a contributor (as done in other .Rmd files
• Modify the DESCRIPTION to add yourself as a contributor
• Replace links to packages with calls to the BiocStyle function that writes the canonical links.

[villafup]

• 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.