Replace a Sweave vignette with an R Markdown vignette

[jwokaty]

Hello Outreachy applicants!

Note: This task can be complete by multiple Outreachy applicants.

This second contribution task builds on what you've learned by working on a Bioconductor package vignette.

Prep Work

• Please read our contribution document, which gives a good overview of the project plus the general workflow. In particular, you will be performing the tasks from Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw).
• Install pandoc

Contribution Task

Make a pull request replacing a Sweave vignette with an R Markdown vignette.

1. Select a vignette from our project board that is labeled 'Easy' or 'Medium', set to 'Todo' and are unassigned.
2. Write a comment with the path of the vignette you'd like to do--e.g., BiocParallel/vignettes/Introduction_To_BiocParallel.Rnw to @Bioconductor/sweave2rmd. We will write your GitHub username as 'Assigned' and set 'Last Modified' to today.x
3. Perform the steps in Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw). Note: You do not need to contact the maintainers to work on this set of vignettes as they have either been previously contact OR they are maintained by the Bioconductor Core Team.
4. Make sure that you request a review by writing @Bioconductor/sweave2rmd in a comment so that we can review your pull request. For example, @Bioconductor/sweave2rmd please review my contribution for Outreachy.
5. If you receive any feedback requesting changes, please address them.

Tip: You can find the PDF you'll be replacing by visiting the landing page for the package under Documents. You can look up the package at Bioconductor Software Packages.

If your pull request is good, it will be merged into Bioconductor!

Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2022-internship-round/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/.

[BeatriceTA]

Hi, @jwokaty
Thank you for the detailed explanation of how to make a contribution. I intend to work on this project and make my contribution soonest

[niyolynate]

Hello, @jwokaty
I intend to work on this issue, am an Outreacy applicant. starting as soon as possible.

[niyolynate]

Hi, i intend to edit this package to a Rmarkdown, [Sweave2Rmd](https://bioconductor.org/packages/release/bioc/html/biocViews.html)
You'll also need to bump the version number in your DESCRIPTION file so that the build machines will
recognize that a new version is available.

Thanks for your time.

[niyolynate]

Please Guide me am i on the right truck choosing this package to edit?
Replace a Sweave vignette with an R Markdown vignette #32

[https://bioconductor.org/packages/release/bioc/html/biocViews.html]

[hsadia538]

Hi @jwokaty
I have created a PR under biobase package for this task

[jwokaty]

Hi @niyolynate, I've updated the instructions above with the link to the project board where you can select a vignette to work on.

[hsadia538]

Hello @jwokaty,
Can you assign me to the vignette Biobase/vignettes/BiobaseDevelopment.Rnw on the board? I am working on it. Thanks.

I see that you have edited the description, when I tried to add a comment in my PR with @Bioconductor/sweave2rmd it was not linking for some reason.

[hsadia538]

Hi @jwokaty ,
I have opened another PR for Biobase/vignettes/BiobaseDevelopment.Rnw Can you please update the board ?
Also, I want to get assigned to Biostrings/vignettes/matchprobes.Rnw. Thanks :)

[BeatriceTA]

Hello @jwokaty,
Can you assign me to graph/vignettes/graph.Rnw on the board? I am working on it.
Thank you

[phyleria]

Hi @jwokaty

Can you kindly assign me to BiocParallel/Vignettes/Introduction_ToBiocParallel.Rnw as I'm working on it. Thanks!

[jwokaty]

Hi, I just wanted to clarify that you do not need to contact any maintainers from the filtered project board. We have already sorted this out because it usually takes time to get approval and we wanted to make sure you would have time to focus on your contribution without any delays. When you start on your vignette, you start from step 3 above Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw).

[phyleria]

Hi, I just wanted to clarify that you do not need to contact any maintainers from the filtered project board. We have already sorted this out because it usually takes time to get approval and we wanted to make sure you would have time to focus on your contribution without any delays. When you start on your vignette, you start from step 3 above Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw).

Thank you for clarifying this @jwokaty !