Convert IRangesOverview.Rnw to IRangesOverview.Rmd

[sonali8434]

@jwokaty please review this PR I have reviewed it once using the checklist and make sure that R CMD build contains html. After your review we will ask @hpages for final review.

Note: The plots position is quite different in the html document but I believe that in the pdf plots are appeared at the middle of the code blocks which is not possible to generate in html the current position of plots look good to me.

Attached
PDF
HTML for your reference.

[sonali8434]

We will be using this checklist to review my PR I have reviewed it myself, Please review my changes and let me know if any more changes are required any suggestion will be appreciated.

Note: During the review I noticed that pdf has

> if (!require("BiocManager"))
+ install.packages("BiocManager")
> BiocManager::install("IRanges")

I Remember that One of the requirements of a vignette is that it must not install anything without the user's knowledge. But the code label uses eval=FALSE to stop running that code chunk so I think there is no problem.

• 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.

• Refer to the contribution guide for acceptable formats

[jwokaty]

@hpages This is just a suggestion, but maybe this section 366-385 can be removed?

[sonali8434]

I have not yet removed it. I will remove it after receiving confirmation from @hpages.

[hpages]

Sure, please remove. These are placeholders that were intended to be filled with something at some point but it never happened. Thx!

[sonali8434]

Done

[jwokaty]

Hi @sonali8434 Thank you for your PR. I noticed a few more places where pandoc didn't convert an expression correctly. Otherwise, everything looks really good and it will be ready for Herve after you address these changes.

[sonali8434]

@jwokaty, thank you for your thorough review. I have incorporated all of your suggested changes, except for this one. Please inform me if any further modifications are needed.

[jwokaty]

Thanks, @sonali8434! I think this ready for @hpages.