Replace a Sweave Vignette With an R Markdown Vignette

[villafup]

Hello Outreachy applicants!

Note: This task can be completed by multiple Outreachy applicants. Please choose this as your second (optional) contribution task to the Bioconductor Sweave2Rmd project as it builds upon the familiarity quiz in the Sweave2Rmd first contribution.

Prep Work

• Sweave2Rmd Knowledge Check
• 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. (As a FYI, although there is no maximum # of vignettes you're allowed to convert, project leads must review everyone's first PR before we are able to assess any additional vignettes from anyone contributing to the project).
2. Write a comment with the path of the vignette you'd like to do--e.g., BiocParallel/vignettes/Introduction_To_BiocParallel.Rnw. We will write your GitHub username as 'Assigned' and set 'Last Modified' to today.
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 contacted 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. Make a comment in this issue with a link to your PR.
6. 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. Tip: You can read how we review PRs in the contribution document. Use the checklist to assess if your PR will pass review.

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-may-2023-internship-cohort/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/.

[Khadeeejah]

I would be working on this vignette:genefilter/vignettes/howtogenefilter.Rnw

Thanks

[devbird007]

Hello, I would like to work on this vignette: genefilter/vignettes/howtogenefinder.Rnw

[alatiku]

I would like to work on the following vignette - graph/vignettes/graph.Rnw

[sonali8434]

Hello, I would like to work on this vignette: Rsamtools/vignettes/Rsamtools-Overview.Rnw please assign me this.

[Reece11]

Hi @villafup I am working on this vignette: GeneMeta/vignettes/GeneMeta.Rnw please assign me thank you

[mcarlsn]

hi hi all - quick plug that for those of you who are interested in getting started on Sweave2Rmd contribution tasks, please start with the first contribution task (instructions here). Once completed, you have the option of then starting the second (optional) contribution task, detailed above, in which you claim a vignette from the project board and convert it. The first contribution task is designed as a ramp to the second task, which is why we ask that you work on them sequentially. When you post here to claim a vignette, please let us know that you've completed the first contribution task. Let us know if you have any questions!

[jwokaty]

@mcarlsn Thanks for the suggestion.

The first task will help set you up for success. Please consider doing it if you haven't already as we tried to highlight important parts of our work that are easily missed.

I've assigned everyone their requested vignettes. We'll update the board with more vignettes later in the week.

[kemicky]

Hi, please I am working on : GenomicAlignments/vignettes/summarizeOverlaps.Rnw Kindly please assign it to me, thank you

[devbird007]

Hello, I would like to work on this vignette: genefilter/vignettes/howtogenefinder.Rnw

I have taken the familiarity quiz and would now commit to the task assigned to me.

[MonalikaPatnaik]

Heyy.. I would like to work on the vignette: GenomicAlignments/vignettes/summarizeOverlaps.Rnw Kindly assign this to me!

[kemicky]

@MonalikaPatnaik : That is the one I am working on just waiting for it to be assigned to me.

[alatiku]

I would like to work on the following vignette - graph/vignettes/graph.Rnw

I have submitted the Quiz for Task 1 and will be proceeding to complete Task 2

[MonalikaPatnaik]

@MonalikaPatnaik : That is the one I am working on just waiting for it to be assigned to me.

Oh okayy..Are there any open issues to work on in the project board under outreachy label, I found all the issues have already been assigned. I have completed my first contribution and looking for the issue to contribute on!

[Reece11]

I've assigned everyone their requested vignettes. We'll update the board with more vignettes later in the week. @MonalikaPatnaik i think this answers your querry here

[MonalikaPatnaik]

Thanks @Reece11 for clarification!

[kemicky]

@MonalikaPatnaik : That is the one I am working on just waiting for it to be assigned to me.

Oh okayy..Are there any open issues to work on in the project board under outreachy label, I found all the issues have already been assigned. I have completed my first contribution and looking for the issue to contribute on!

Hi,I understand we can work on the same project , I am a novice here to am just getting around with the task, learning and understanding the task. so I guess it ok ..

[kemicky]

@MonalikaPatnaik : I will explain to you how we are to do the steps for how we are to complete task 1 when I am done. cheers.

[devbird007]

Hello, I would like to work on this vignette: genefilter/vignettes/howtogenefinder.Rnw

I have taken the familiarity quiz and would now commit to the task assigned to me.

Hi @jwokaty I have completed the task assigned to me and submitted a pull request for it. Next I would like to be assigned this task: Category/vignettes/ChromBand.Rnw

[jwokaty]

Hello, I would like to work on this vignette: genefilter/vignettes/howtogenefinder.Rnw

I have taken the familiarity quiz and would now commit to the task assigned to me.

Hi @jwokaty I have completed the task assigned to me and submitted a pull request for it. Next I would like to be assigned this task: Category/vignettes/ChromBand.Rnw

@devbird007 Rather than start on a new task, I am going to ask you to review your work with https://bioconductor.github.io/sweave2rmd/articles/contribute.html#review-a-pull-request. I'll flag your PR for review, which may take a few days. You should address any changes made by the reviewer. This is especially important for the first PR so you don't make the same mistakes in subsequent PRs. Once it is merged, you can start a new task.

[jwokaty]

I would like to work on the following vignette - graph/vignettes/graph.Rnw please assign me this .

@sonali8434 Since graph is already assigned, I'll assign you to GenomicFiles/vignettes/GenomicFiles.Rnw as you discussed and remove you from Rsamtools/vignettes/Rsamtools-Overview.Rnw.

[iamatifmoin]

I will be working on:

ACME/vignettes/ACME.Rnw

I have completed the first contribution task. Thanks.

[sonali8434]

I would like to work on the following vignette - graph/vignettes/graph.Rnw please assign me this .

@sonali8434 Since graph is already assigned, I'll assign you to GenomicFiles/vignettes/GenomicFiles.Rnw as you discussed and remove you from Rsamtools/vignettes/Rsamtools-Overview.Rnw.

Hi @jwokaty I have completed the 2nd task assigned to me GenomicFiles/vignettes/GenomicFiles.Rnw and submitted a pull request for it please review my PR link- https://github.com/Bioconductor/GenomicFiles/pull/7 and let me Know what to do next.

I can work on Category/vignettes/ChromBand.Rnw in the remaining time if you assign me this.

Thanks ..

[MonalikaPatnaik]

@MonalikaPatnaik : I will explain to you how we are to do the steps for how we are to complete task 1 when I am done. cheers.

Sure..Thankyou:)

[jwokaty]

I wanted to mention a few important things.

1. Please do the knowledge quiz at https://github.com/Bioconductor/sweave2rmd/issues/62. It will prepare you for this task and we will review the responses. You'll get feedback at the email associated with your response. This email should ideally match the one you used for Outreachy so we can verify you did it if you include it in your contributions.
2. Please only select vignettes from the project board at https://github.com/orgs/Bioconductor/projects/2/views/6. We selected these vignettes specifically because they're maintained by the Bioconductor Core Team; these packages and vignettes are not deprecated; etc., so that we can control merging the PR. If you pick a vignette that is not maintained by the core team, we can review the PR but we will ultimately have no control over merging it because it is up to the maintainer since the contribution is to their Bioconductor package. We will add more vignettes to the board soon.
3. If you finish this task, your first PR needs to go through review. This will take time, so be patient and proactive by using the checklist to perform your own review first: https://bioconductor.github.io/sweave2rmd/articles/contribute.html#review-a-pull-request. This way you won't make the same mistake on your second PR. You could also look at some vignettes in other packages, so that you start to see the general format of R Markdown, such as https://github.com/Bioconductor/BiocHubsShiny or https://github.com/Bioconductor/graph.

[jwokaty]

I will be working on:

ACME/vignettes/ACME.Rnw

I have completed the first contribution task. Thanks.

@iamatifmoin Please choose a vignette from the board filtered for Outreachy: https://github.com/orgs/Bioconductor/projects/2/views/6. We'll be adding more vignettes soon.

[jwokaty]

I would like to work on the following vignette - graph/vignettes/graph.Rnw please assign me this .

@sonali8434 Since graph is already assigned, I'll assign you to GenomicFiles/vignettes/GenomicFiles.Rnw as you discussed and remove you from Rsamtools/vignettes/Rsamtools-Overview.Rnw.

Hi @jwokaty I have completed the 2nd task assigned to me GenomicFiles/vignettes/GenomicFiles.Rnw and submitted a pull request for it please review my PR link- Bioconductor/GenomicFiles#7 and let me Know what to do next.

I can work on Category/vignettes/ChromBand.Rnw in the remaining time if you assign me this.

Thanks ..

@sonali8434 Please see suggestion 3 in https://github.com/Bioconductor/sweave2rmd/issues/63#issuecomment-1460834595.

[Reece11]

I wanted to mention a few important things.

1. Please do the knowledge quiz at Sweave2Rmd Knowledge Check #62. It will prepare you for this task and we will review the responses. You'll get feedback at the email associated with your response. This email should ideally match the one you used for Outreachy so we can verify you did it if you include it in your contributions.
2. Please only select vignettes from the project board at https://github.com/orgs/Bioconductor/projects/2/views/6. We selected these vignettes specifically because they're maintained by the Bioconductor Core Team; these packages and vignettes are not deprecated; etc., so that we can control merging the PR. If you pick a vignette that is not maintained by the core team, we can review the PR but we will ultimately have no control over merging it because it is up to the maintainer since the contribution is to their Bioconductor package. We will add more vignettes to the board soon.
3. If you finish this task, your first PR needs to go through review. This will take time, so be patient and proactive by using the checklist to perform your own review first: https://bioconductor.github.io/sweave2rmd/articles/contribute.html#review-a-pull-request. This way you won't make the same mistake on your second PR. You could also look at some vignettes in other packages, so that you start to see the general format of R Markdown, such as https://github.com/Bioconductor/BiocHubsShiny or https://github.com/Bioconductor/graph.

@jwokaty well noted

[kemicky]

@jwokaty : Thank you everyone, Thank you for your clarification. If I may just clarify the project I initially choose to work for my first task : GenomicAlignments/vignettes/summarizeOverlaps.Rnw The maintainer is not Bioconductor After your instructions update now, Do I need to change it to one that has Bioconductor has maintainer as per your instructions ?. If Yes, Kindly advice and I am very happy to quickly change it. Thank you all for your patience.

[kemicky]

@jwokaty: Please may you kindly update my assignment, I have chosen a new project maintained by Bioconductor Core Team as instructed and please remove me from the one I chose before . Please may you kindly assign to me: Category/vignettes/ChromBand.Rnw Thank you all

[iamatifmoin]

I will be working on:

ACME/vignettes/ACME.Rnw

I have completed the first contribution task. Thanks.

@iamatifmoin Please choose a vignette from the board filtered for Outreachy: https://github.com/orgs/Bioconductor/projects/2/views/6. We'll be adding more vignettes soon.

@jwokaty Okay!

I'll be doing this one:

GOstats/vignettes/GOstatsForUnsupportedOrganisms.Rnw

[devbird007]

Hello, I would like to work on this vignette: genefilter/vignettes/howtogenefinder.Rnw

I have taken the familiarity quiz and would now commit to the task assigned to me.

Hi @jwokaty I have completed the task assigned to me and submitted a pull request for it. Next I would like to be assigned this task: Category/vignettes/ChromBand.Rnw

@devbird007 Rather than start on a new task, I am going to ask you to review your work with https://bioconductor.github.io/sweave2rmd/articles/contribute.html#review-a-pull-request. I'll flag your PR for review, which may take a few days. You should address any changes made by the reviewer. This is especially important for the first PR so you don't make the same mistakes in subsequent PRs. Once it is merged, you can start a new task.

I have reviewed my work myself with the link you sent. I will now await feedback from my reviewer. Thanks.

[Rohit-Satyam]

Hi @villafup I am working on this vignette geneplotter/vignettes/byChroms.Rnw and geneplotter/vignettes/visualize.Rnw. Please assign me

Thank you

[alatiku]

@Bioconductor/sweave2rmd please review my work. I created the RMarkdown file for the graph vignette and created a pull request for the changes made to my branch.

[jwokaty]

Hi @villafup I am working on this vignette geneplotter/vignettes/byChroms.Rnw and geneplotter/vignettes/visualize.Rnw. Please assign me

Thank you

@Rohit-Satyam Can I ask you to select 1 to work on? We'll review the PR completely before you get another vignette.

[jwokaty]

If you finish your PR, please make a comment with the link to your PR. Thank you :)

[devbird007]

If you finish your PR, please make a comment with the link to your PR. Thank you :)

This is my pull request here: https://github.com/Bioconductor/genefilter/pull/10

[sonali8434]

Hello, @jwokaty my PR link is incorrect in https://github.com/orgs/Bioconductor/projects/2/views/6 my correct PR link is https://github.com/Bioconductor/GenomicFiles/pull/8 please update the link in the project board. Thank you .

[alatiku]

If you finish your PR, please make a comment with the link to your PR. Thank you :)

Hi, please here is the link to my Pull Request https://github.com/Bioconductor/graph/pull/16

Please take note this is a new pull request. Thank you

[Daviskojob]

I would be working on this vignette bioDist/vignettes/bioDist.Rnw

[Dbn-tech]

hello @jwokaty , i would like to work on this vignette geneplotter/vignettes/byChroms.Rnw

[SunSummoner]

Hii @jwokaty I would be working on geneplotter/vignettes/byChroms.Rnw Thank you

[jwokaty]

@Rohit-Satyam Which vignette are you working on?

[jwokaty]

@Dbn-tech @SunSummoner I am trying to determine if someone is already working on this vignette, so you may have to choose other. Or maybe you want to go ahead and choose another so that you don't have to wait.

[kemicky]

Hello everyone: Good day Please I am having file does not exist error while using : pandoc -f latex -t markdown file.Rnw -o file.Rmd in RStudio. I have installed rmarkdown and latex (tinytex) Any suggestion please, thank you

[Dbn-tech]

hello again @jwokaty ...i would like to work on this GOstats/vignettes/GOstatsHyperG.Rnw as you solve the issue on who is working on the other vignette

[alatiku]

If you finish your PR, please make a comment with the link to your PR. Thank you :)

Hi, please here is the link to my Pull Request Bioconductor/graph#16

Please take note this is a new pull request. Thank you

Hi, my new PR is ready. https://github.com/Bioconductor/graph/pull/18 Thank you so much.

[jwokaty]

@kemicky It might be better to copy paste the command and the error or show a screenshot in slack. Can you put it there and "@" mention me so that I get notified when you post it?

[Khadeeejah]

Hi this is the link to my pr @jwokaty https://github.com/Bioconductor/genefilter/pull/11

[kemicky]

@kemicky It might be better to copy paste the command and the error or show a screenshot in slack. Can you put it there and "@" mention me so that I get notified when you post it?

@jwokaty : ok

[Khadeeejah]

Hi this is the link to my pr @jwokaty Bioconductor/genefilter#11

@jwokaty