Sweave2Rmd Knowledge Check

[villafup]

Welcome Outreachy applicants!

Note: Multiple Outreachy applicants can work on this issue.

Please choose this as your first contribution task to the Bioconductor Sweave2Rmd project as it will familiarize you with the R, R Markdown, GitHub processes, documentation, and the Sweave2Rmd conversion process (learn more about Bioconductor here).

Sweave2Rmd Project

Sweave2Rmd is a community project to convert Sweave vignettes to Rmd. Currently, there are approximately 900 vignettes .Rnw in software packages. These vignettes do not operate as effectively as .Rmd as they are older, combine latex with R, and compile to PDF whereas .Rmd vignettes compile to HTML, are BiocStyle compatible, and easier to read and maintain. Therefore, the aim of the Sweave2Rmd project is to convert these Sweave vignettes to .Rmd.

Prep Work

If you're not familiar with R and R Markdown, please learn a little about them. The following links should be sufficient to get you started: R Primer - Programming basics or R Markdown. Then you may complete the following steps:

• Install R
• Install RStudio
• In RStudio or through the terminal, install devtools and BiocManager: install.packages(c("devtools", "BiocManager"))
• Read through the Sweave2Rmd Contribute article, which explains step-by-step the process of converting a Sweave document to Rmd. The article will be important for completing this contribution task.

Contribution Task

After reading the Sweave2Rmd Contribute article, you may complete the 2023 Outreachy Sweave2Rmd Contribution Familiarity Quiz. The quiz contains questions about the process of converting a Sweave vignette to Rmd. It is an opportunity to both test your familiarity with the Contribute article and learn how to convert a vignette if you choose to complete the second (optional) contribution task. We expect the quiz to take up to 3 hours to complete. Only your first submission will count. If you have any questions about the quiz, feel free to post on the Sweave2Rmd Outreachy Slack channel. To join the Slack channel, view https://slack.bioconductor.org/ then search for the channel #outreachy.

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]

Hi @villafup I am an outreachy intern here i would like to work on this issue. kindly assign it to me. thanks

[jwokaty]

Hi @villafup I am an outreachy intern here i would like to work on this issue. kindly assign it to me. thanks

@Khadeeejah Multiple applicants can work on this issue, no assignment needed! :)

[siddhi-244]

Will work on this !

[Reece11]

Hi @jwokaty I am an outreachy intern , and i am working on this!

[kemicky]

@jwokaty Hello Sir, My name is Mary Jones an Outreachy intern and I currently am working on this contribution, may you please assign this to me. thank you for anticipating to give me the opportunity.

[SunSummoner]

Welcome Outreachy applicants!

Note: Multiple Outreachy applicants can work on this issue.

Please choose this as your first contribution task to the Bioconductor Sweave2Rmd project as it will familiarize you with the R, R Markdown, GitHub processes, documentation, and the Sweave2Rmd conversion process (learn more about Bioconductor here).

Sweave2Rmd Project

Sweave2Rmd is a community project to convert Sweave vignettes to Rmd. Currently, there are approximately 900 vignettes .Rnw in software packages. These vignettes do not operate as effectively as .Rmd as they are older, combine latex with R, and compile to PDF whereas .Rmd vignettes compile to HTML, are BiocStyle compatible, and easier to read and maintain. Therefore, the aim of the Sweave2Rmd project is to convert these Sweave vignettes to .Rmd.

Prep Work

If you're not familiar with R and R Markdown, please learn a little about them. The following links should be sufficient to get you started: R Primer - Programming basics or R Markdown. Then you may complete the following steps:

• Install R
• Install RStudio
• In RStudio or through the terminal, install devtools and BiocManager: install.packages(c("devtools", "BiocManager"))
• Read through the Sweave2Rmd Contribute article, which explains step-by-step the process of converting a Sweave document to Rmd. The article will be important for completing this contribution task.

Contribution Task

After reading the Sweave2Rmd Contribute article, you may complete the 2023 Outreachy Sweave2Rmd Contribution Familiarity Quiz. The quiz contains questions about the process of converting a Sweave vignette to Rmd. It is an opportunity to both test your familiarity with the Contribute article and learn how to convert a vignette if you choose to complete the second (optional) contribution task. We expect the quiz to take up to 3 hours to complete. If you have any questions about the quiz, feel free to post on the Sweave2Rmd Outreachy Slack channel. To join the Slack channel, view https://slack.bioconductor.org/ then search for the channel #outreachy.

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/

Hi I am Kritika Verma. I am an Outreachy applicant for the may cohort and I would like to work on this as my first contribution. Thank you.

[kemicky]

Hello please I am trying to claim one of the claim a vigennette, please can you assign this medium to me : summarizeOverlaps.Rnw to me . I am unable to assign the project to me.

[Palaktahlyani]

Hey @jwokaty I am Outreachy intern, working on this project. Hope to get connect with you all.

[sonali8434]

Hi @jwokaty I am an outreachy intern , and i am working on this , My first contribution task is completed currently working on 2nd contribution task.

[Reece11]

Hi @jwokaty I am an outreachy intern , and i am working on this!

hi @jwokaty I completed the first task moving to completing the second contribution task

[Merit25]

Welcome Outreachy applicants!

Note: Multiple Outreachy applicants can work on this issue.

Please choose this as your first contribution task to the Bioconductor Sweave2Rmd project as it will familiarize you with the R, R Markdown, GitHub processes, documentation, and the Sweave2Rmd conversion process (learn more about Bioconductor here).

Sweave2Rmd Project

Sweave2Rmd is a community project to convert Sweave vignettes to Rmd. Currently, there are approximately 900 vignettes .Rnw in software packages. These vignettes do not operate as effectively as .Rmd as they are older, combine latex with R, and compile to PDF whereas .Rmd vignettes compile to HTML, are BiocStyle compatible, and easier to read and maintain. Therefore, the aim of the Sweave2Rmd project is to convert these Sweave vignettes to .Rmd.

Prep Work

If you're not familiar with R and R Markdown, please learn a little about them. The following links should be sufficient to get you started: R Primer - Programming basics or R Markdown. Then you may complete the following steps:

• Install R
• Install RStudio
• In RStudio or through the terminal, install devtools and BiocManager: install.packages(c("devtools", "BiocManager"))
• Read through the Sweave2Rmd Contribute article, which explains step-by-step the process of converting a Sweave document to Rmd. The article will be important for completing this contribution task.

Contribution Task

After reading the Sweave2Rmd Contribute article, you may complete the 2023 Outreachy Sweave2Rmd Contribution Familiarity Quiz. The quiz contains questions about the process of converting a Sweave vignette to Rmd. It is an opportunity to both test your familiarity with the Contribute article and learn how to convert a vignette if you choose to complete the second (optional) contribution task. We expect the quiz to take up to 3 hours to complete. If you have any questions about the quiz, feel free to post on the Sweave2Rmd Outreachy Slack channel. To join the Slack channel, view https://slack.bioconductor.org/ then search for the channel #outreachy.

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/

I am an outreachy intern, I would like to contribute on the first contribution task

[jwokaty]

I noticed that so far that very few people have answered the following questions correctly, which might be due to wording, so I am providing additional hints:

• How do you link to Bioconductor packages? What we're looking for is a best practice that is described in one of the tips to get the canonical URL for a package. Since Bioconductor has a release every six months, links can quickly go stale.

• Can you install packages packages in vignettes? Again, read the tip provided, which goes to the Bioconductor package documentation. All packages submitted to Bioconductor must conform the guidance in the documentation.

Please also remember to allow access to the files you uploaded, which are in your google drive.

[Dbn-tech]

Hey @jwokaty I am Outreachy intern, working on this project. Hope to get connect with you all.

[mcarlsn]

Hi @jwokaty I am an outreachy intern , and i am working on this! FYI @Reece11 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[mcarlsn]

FYI @sonali8434 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[mcarlsn]

@jwokaty Hello Sir, My name is Mary Jones an Outreachy intern and I currently am working on this contribution, may you please assign this to me. thank you for anticipating to give me the opportunity.

FYI @kemicky your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[mcarlsn]

FYI @Rohit-Satyam your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[Dbn-tech]

Hello @mcarlsn i also submitted mine, i hope it was received

[mcarlsn]

Hi @villafup I am an outreachy intern here i would like to work on this issue. kindly assign it to me. thanks

FYI @Khadeeejah your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[Khadeeejah]

Hi @villafup I am an outreachy intern here i would like to work on this issue. kindly assign it to me. thanks

FYI @Khadeeejah your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

Thank you very much I would do that right away.

[mcarlsn]

FYI @sirjoka your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[mcarlsn]

FYI @bellatrick your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[bellatrick]

FYI @bellatrick your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

Thanks a lot, will do!!!

[mcarlsn]

Hello @mcarlsn i also submitted mine, i hope it was received

FYI @Dbn-tech your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[kemicky]

@jwokaty Hello Sir, My name is Mary Jones an Outreachy intern and I currently am working on this contribution, may you please assign this to me. thank you for anticipating to give me the opportunity.

FYI @kemicky your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

@mcarlsn Thank you very much Ma'am/ Sir, I will do so immediately

[Oluwabukolab]

Hi @mcarlsn I just completed the quiz and submited. Please acknowledge!

[mcarlsn]

Hi @mcarlsn I just completed the quiz and submited. Please acknowledge!

FYI @Bukolab99 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. (FYI you can disregard the notifications that this was closed and reopened - accident!) Thanks

[kemicky]

@jwokaty Good day everyone: please here is my PR for review: https://github.com/Bioconductor/Category/pull/4 thank you

[OpehJanet20]

Hello, I am Janet Solomon, an Outreachy applicant for May 2023 cohort. I will like to work on this as my first contribution. Thank you.

[OpehJanet20]

@jwokaty Hello Sir, My name is Janet Solomon an Outreachy applicant for may 2023 cohort and I currently am working on this as my first contribution, Please assign this to me. Thank you.

[mcarlsn]

Hello, I am Janet Solomon, an Outreachy applicant for May 2023 cohort. I will like to work on this as my first contribution. Thank you.

Welcome, Janet! You're more than welcome to start the quiz whenever you'd like. It is open to anyone without being explicitly assigned. Please let us know if you have any questions

[mcarlsn]

FYI @maryjon4 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[mcarlsn]

FYI @viclaty (email user name) your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[mcarlsn]

FYI @sopeadeniji your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. Thanks!

[Oluwabukolab]

Hi @mcarlsn I just completed the quiz and submited. Please acknowledge!

FYI @Bukolab99 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. (FYI you can disregard the notifications that this was closed and reopened - accident!) Thanks

Hello @mcarlsn I am @viclaty (email username) you've acknowledged my submission over a week ago.

[mcarlsn]

Hi @mcarlsn I just completed the quiz and submited. Please acknowledge!

FYI @Bukolab99 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. (FYI you can disregard the notifications that this was closed and reopened - accident!) Thanks

Hello @mcarlsn I am @viclaty (email username) you've acknowledged my submission over a week ago.

Apologies! Crossed wires there.

[Oluwabukolab]

Hi @mcarlsn I just completed the quiz and submited. Please acknowledge!

FYI @Bukolab99 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. (FYI you can disregard the notifications that this was closed and reopened - accident!) Thanks

Hello @mcarlsn I am @viclaty (email username) you've acknowledged my submission over a week ago.

Apologies! Crossed wires there.

Not a problem. Have a good day!

[mcarlsn]

Hi @mcarlsn I just completed the quiz and submited. Please acknowledge!

FYI @Bukolab99 your submitted form was received. You may use the URL to this comment as evidence in the Outreachy application of completing the first contribution. (FYI you can disregard the notifications that this was closed and reopened - accident!) Thanks

Hello @mcarlsn I am @viclaty (email username) you've acknowledged my submission over a week ago.

Apologies! Crossed wires there.

Not a problem. Have a good day!

You too!

[devbird007]

Hi @jwokaty @mcarlsn @villafup I completed the first quiz and mentioned it here, but I did not know that I would have needed to reference it here at that time so I could reference it when recording my contribution.

Please what do I do?

[Khadeeejah]

Hi @jwokaty @mcarlsn @villafup

I completed the first quiz and mentioned it here, but I did not know that I would have needed to reference it here at that time so I could reference it when recording my contribution.

Please what do I do?

You can copy the link to this comment Or also copy the link to the docs concerning your response in the mail @mcarlsn sent us some week back

[devbird007]

Hi @jwokaty @mcarlsn @villafup I completed the first quiz and mentioned it here, but I did not know that I would have needed to reference it here at that time so I could reference it when recording my contribution. Please what do I do?

You can copy the link to this comment Or also copy the link to the docs concerning your response in the mail @mcarlsn sent us some week back

By "link to the docs concerning your response in the mail", do you mean the google doc file containing our quiz result that I received from Madelyn?

[Khadeeejah]

Hi @jwokaty @mcarlsn @villafup

I completed the first quiz and mentioned it here, but I did not know that I would have needed to reference it here at that time so I could reference it when recording my contribution.

Please what do I do?

You can copy the link to this comment Or also copy the link to the docs concerning your response in the mail @mcarlsn sent us some week back

By "link to the docs concerning your response in the mail", do you mean the google doc file containing our quiz result that I received from Madelyn?

Yes that , however @mcarlsn has already received all our submission and linked our GitHub nanes to our submission. So you are good

[devbird007]

Alright thanks

[mcarlsn]

Hi @jwokaty @mcarlsn @villafup I completed the first quiz and mentioned it here, but I did not know that I would have needed to reference it here at that time so I could reference it when recording my contribution.

Please what do I do?

@devbird007 Thanks for posting. In your final application, you may use the link to the previous post or URL for this to show that you completed the first contribution for this project. Thank you for submitting the knowledge check quiz! Please let me know if you have any questions.

[devbird007]

Hi @jwokaty @mcarlsn @villafup I completed the first quiz and mentioned it here, but I did not know that I would have needed to reference it here at that time so I could reference it when recording my contribution. Please what do I do?

@devbird007 Thanks for posting. In your final application, you may use the link to the previous post or URL for this to show that you completed the first contribution for this project. Thank you for submitting the knowledge check quiz! Please let me know if you have any questions.

Thank you