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/.

[jwokaty]

@SunSummoner I am sorry for the delayed response. I am trying to clarify with @Rohit-Satyam what vignette they are working on. If they are not working on the vignette you requested, I will give it to you; however, it may be better to select another vignette so that you can continue.

[SunSummoner]

Hi @jwokaty As you said about the uncertainty regarding whose working with the geneplotter vignette. I'd like to change my vignette and work with ShortRead/vignettes/Overview.Rnw. Thank you

[bellatrick]

Hi, @jwokaty. I'd like to work on this vignette Rsamtools/vignettes/Rsamtools-Overview.Rnw

[jwokaty]

@bellatrick I'll assign you this vignette. It has an issue that I've discussed at https://community-bioc.slack.com/archives/C037LN1HQDB/p1678601431723939?thread_ts=1678564533.972929&cid=C037LN1HQDB.

[bellatrick]

@bellatrick I'll assign you this vignette. It has an issue that I've discussed at https://community-bioc.slack.com/archives/C037LN1HQDB/p1678601431723939?thread_ts=1678564533.972929&cid=C037LN1HQDB.

Thank you @jwokaty ,I will go through the discussion

[alatiku]

@jwokaty Good morning. Please do review my PR when free. https://github.com/Bioconductor/graph/pull/18

Thank you

[alatiku]

@jwokaty new PR https://github.com/Bioconductor/graph/pull/19 Please review. Thank you

[Dbn-tech]

Hello @jwokaty, i have completed the second contribution and I would like you to review it and advise where necessary. https://github.com/Bioconductor/GOstats/pull/2 Thank you

[Rohit-Satyam]

@SunSummoner I am sorry for the delayed response. I am trying to clarify with @Rohit-Satyam what vignette they are working on. If they are not working on the vignette you requested, I will give it to you; however, it may be better to select another vignette so that you can continue.

Sorry for late reply, I just pushed the changes for geneplotter/vignettes/byChroms.Rnw only as you asked to do only single vignette.

pull request

[jwokaty]

@BerylKanali Could I ask you to review https://github.com/Bioconductor/geneplotter/pull/2 for @Rohit-Satyam?

@Dbn-tech I have asked @villafup to review https://github.com/Bioconductor/GOstats/pull/2

[bellatrick]

@jwokaty , hi, I opened a PR on Rsamtools Can I get a review whenever you're available?

[BerylKanali]

@BerylKanali Could I ask you to review Bioconductor/geneplotter#2 for @Rohit-Satyam?

@Dbn-tech I have asked @villafup to review Bioconductor/GOstats#2

@jwokaty Sure.

[devbird007]

@jwokaty I'd love to be assigned this task RBGL/vignettes/RBGL.Rnw from the project board. :-)

[sonali8434]

@jwokaty Please assign me GOstats/vignettes/GOvis.Rnw from project board. Thank you.

[sopeadeniji]

@jwokaty Please assign me geneplotter/vignettes/visualize.Rnw on project board. Thanks.

[Dbn-tech]

Hello @jwokaty, i have completed the second contribution and I would like you to review it and advise where necessary. Bioconductor/GOstats#2 Thank you

I have made the corrections requested, and I would like to know if there is anything else needed as I would like to work on another Rnw file @jwokaty @villafup

[devbird007]

Hello @jwokaty

This is my pull request here: https://github.com/Bioconductor/RBGL/pull/3

I also made sure to ensure it builds successfully.

[sonali8434]

@jwokaty Please assign me GOstats/vignettes/GOvis.Rnw from project board. Thank you.

Hello @jwokaty this is my pull request for the above stated .Rnw to .Rmd conversion. https://github.com/Bioconductor/GOstats/pull/3

[Oluwabukolab]

@jwokaty Hi I would like to work on this vignette: chipseq/vignettes/Workflow.Rnw. Please assign me. Thank you

[Oluwabukolab]

@jwokaty Hi I would like to work on this vignette: chipseq/vignettes/Workflow.Rnw. Please assign me. Thank you

@Bukolab99 I think this vignette is already assigned to someone else you have to choose an unassigned vignette from project board https://github.com/orgs/Bioconductor/projects/2/views/6

It is unassigned. Check the first on the list

[mcarlsn]

Bukolab99

FYI you've been assigned chipseq/vignettes/Workflow.Rnw.

[sopeadeniji]

@jwokaty Please, review my pull request at https://github.com/Bioconductor/geneplotter/pull/3 . Thanks

[sonali8434]

@jwokaty Please assign me GOstats/vignettes/GOvis.Rnw from project board. Thank you.

Hello @jwokaty this is my pull request for the above stated .Rnw to .Rmd conversion. Bioconductor/GOstats#3

Please add this pull request in the project board.

[jwokaty]

@sopeadeniji @sonali8434 I've updated the board with your PRs.

[kemicky]

@jwokaty : Good day everyone, @mcarlsn : Good day Ma'am : please may you kindly find the GitHub repo link to the ChromBand Sweave2Rmd for your perusal and review: https://github.com/kemicky/file-Rmd I was not able to create a pull request because the original repo I clone directly from bioconductor site and there was no GitHub repo link for me to fork the repo from. please kindly advice if I must make a push to the original repo as well While I wait for your response and review of this one, I will continue to work on the Category.Rnw file Thank you very much

[jwokaty]

@kemicky I think it might be better to fork the repo, clone it, then copy your files over from your file-Rmd repo to your clone. Let's move this conversation to the sweave2rmd channel on slack. Please message me there.

[kemicky]

@kemicky I think it might be better to fork the repo, clone it, then copy your files over from your file-Rmd repo to your clone. Let's move this conversation to the sweave2rmd channel on slack. Please message me there.

Ok, thank you I have done as you instructed and explained, and made the right pull requestor the GitHub repo for review: https://github.com/Bioconductor/Category/pull/4 thank you all

[devbird007]

Hi @villafup, on the project board, I noticed that you have been assigned my PR. Here is the link to it: https://github.com/Bioconductor/RBGL/pull/3

I look forward to working with you on it.

[Dbn-tech]

Hello, @jwokaty @mcarlsn I would like to work on this last unassigned Pr OrganismDbi/vignettes/OrganismDbi.Rnw(https://github.com/Bioconductor/OrganismDbi) thank you

[Oluwabukolab]

@jwokaty @villafup @mcarlsn Please kindly review my pull request [https://github.com/Bioconductor/chipseq/pull/2]

[alatiku]

Please can I get this vignette OrganismDbi/vignettes/OrganismDbi.Rnw assigned to me

[jwokaty]

@Dbn-tech Your first PR must be merged in order to work on another vignette.

@Bukolab99 I've put your PR on the board.

@sirjoka I can assign it to you.

[Khadeeejah]

@jwokaty is it possible to work on a vignette that has been assigned to someone else but the status has been on "in progress" long ago ?

As there are no more Vignettes to work on .

[jwokaty]

@Khadeeejah I'm hesitant to allow that as they could be working on those vignettes. In the end, I can only merge 1 PR.

I am trying to find more vignettes; however, I have to ask if the maintainer will accept the PRs. I will update the board as I have more and notify here when they are available.

[Khadeeejah]

@Khadeeejah I'm hesitant to allow that as they could be working on those vignettes. In the end, I can only merge 1 PR.

I am trying to find more vignettes; however, I have to ask if the maintainer will accept the PRs. I will update the board as I have more and notify here when they are available.

Noted thank you

[kemicky]

@jwokaty : Good day all, I am almost done with mine. I will PR it by today

[Khadeeejah]

Hello colleagues, some of us are newbies and we are doing our best to get this right. Everyone is doing their best and some of us it takes us all nights and lots of doing this over and over again to get it right . Can you give us a chance and why would anyone want to work on something someone had already done half way cos definitely the person who worked on it that much must have solved some of the work, why want to take over someones else hard work ?!. Please be patient. I am finishing it up. Thank you

Hi based on what I can see on the board. You have a PR already, your task doesn't fall in that category.

I was only referring to issues that do not have prs attached to it and they have been assigned to someone since the beginning of the contribution phase.

You can refer back to my message for clarity.

[kemicky]

Hello colleagues, some of us are newbies and we are doing our best to get this right. Everyone is doing their best and some of us it takes us all nights and lots of doing this over and over again to get it right . Can you give us a chance and why would anyone want to work on something someone had already done half way cos definitely the person who worked on it that much must have solved some of the work, why want to take over someones else hard work ?!. Please be patient. I am finishing it up. Thank you

Hi based on what I can see on the board. You have a PR already, your task doesn't fall in that category.

I was only referring to issues that do not have prs attached to it and they have been assigned to someone since the beginning of the contribution phase.

You can refer back to my message for clarity.

Ok, thank you for clarity.

[sopeadeniji]

@jwokaty I have updated visualize.Rmd @ https://github.com/Bioconductor/geneplotter/pull/3 based on your revisions. Thanks.

[Khadeeejah]

@jwokaty I just saw this on the board

https://github.com/mtmorgan/DirichletMultinomial/blob/master/vignettes/DirichletMultinomial.Rnw

Kindly assign it to me Thank you

[kemicky]

@jwokaty please I see all the vignettes are assigned , please may you assign another unassigned vignettes me thank you.

[alatiku]

@jwokaty Here is my pull request for the OrganismDbi sweave conversion. https://github.com/Bioconductor/OrganismDbi/pull/3

Please have a look when free. Thank you

[sopeadeniji]

@jwokaty visualize.Rmd updated @ https://github.com/Bioconductor/geneplotter/pull/3. Thanks.

[bellatrick]

@jwokaty kindly assign GeneMeta/vignettes/GeneMeta.Rnw to me. I'd like to work on it

[Dbn-tech]

Hello, @jwokaty @mcarlsn I would like to work on this last unassigned Pr OrganismDbi/vignettes/OrganismDbi.Rnw(https://github.com/Bioconductor/OrganismDbi) thank you

hello, @jwokaty @villafup, i would like to know whether there are any other changes needed on my PR kindy..I would like to work on another Rnw after that one is merged

[Dbn-tech]

Hello, @jwokaty @mcarlsn can i work on this kindly. ShortRead/vignettes/Overview.Rnw. At your free time kindly assign it to me