Checklist for package Submission to CRAN/Bioconductor

[gvegayon]

New Core C/D Assessment Project Template

This document provides a general framework for assessing the software and computing needs of a particular project.

The first step consists of answering the following questions:

• [ ] In a paragraph, describe what is the project about.
• [ ] List the project's specific goals (e.g. make the method available for public use, create a web service, present this analysis)
• [ ] Think about what are your computing/software needs, and list them.

Once a general overview of the project has been defined, the next step consists of analyzing the following:

R packages development

Fundamental questions/tasks

• [ ] Check for other R packages/software that does what the project tries to do.
• [ ] Describe the ultimate goal of your R package (e.g. solve an optim problem, implement a visualization problem, estimate parameters, etc.)
• [ ] Think about data (if any needed), in particular, input/output, have you checked any R packages that already have this?
• [ ] Create a repository for the package.

Once the project is on git, following checkmarks

• [ ] The package uses roxygen2 (you can turn your package Rd files to roxygen using Rd2roxygen).
• [ ] The package's functions are thoroughly documented. This includes Description, parameters (@param), value (@return), details (if any), examples (@details), references (@references) and links to other functions (@seealso, and @family).
• [ ] The package has been fully tested using testthat or another framework.
• [ ] The project is built using Continuous Integration services as Travis-ci and Appveyor (use the usethis package to set it up, eg: usethis::use_travis).
• [ ] The package includes a vignette with an extended example and, if needed, references on the package.
• [ ] The package has a website (suggest using pkgdown)

Sending a package to CRAN

Prepare for release:

• [ ] devtools::check_win_devel()
• [ ] rhub::check_for_cran()
• [ ] revdepcheck::revdep_check(num_workers = 4)
• [ ] Polish NEWS
• [ ] If new failures, update email.yml then revdepcheck::revdep_email_maintainers()

Perform release:

• [ ] Bump version (in DESCRIPTION and NEWS)
• [ ] devtools::check_win_devel() (again!)
• [ ] devtools::submit_cran()
• [ ] pkgdown::build_site()
• [ ] Approve email

Wait for CRAN...

• [ ] Tag release
• [ ] Bump dev version

Sending a package to Bioconductor

Prepare for release:

• [ ] Pass R CMD check and R CMD Biocheck
• [ ] Go visit this guidance site
• [ ] Add SSH public key(s) to your GitHub account
• [ ] Add a webhook to your repository
• [ ] Submit by opening a new issue in the Bioconductor Contributions repository.

Perform release:

• [ ] Bump version (in DESCRIPTION and NEWS) which triggers the submission
• [ ] Receive emails about successfully building your package without errors or warnings.
• [ ] A technical review provided by a Bioconductor team member
• [ ] Approve email

[jimb3]

George,

I've only submitted to CRAN using devtools::release(). It asks a bunch of questions about checks that need to be run. I verify each one and then submit. It appears to specify more checks than you listed. Am I doing something wrong or is what I'm doing okay.

John

---

From: George G. Vega Yon notifications@github.com Sent: Thursday, October 1, 2020 2:27 PM To: USCbiostats/AnnoQR AnnoQR@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [USCbiostats/AnnoQR] Checklist for package Submission to CRAN/Bioconductor (#1)

New Core C/D Assessment Project Template

This document provides a general framework for assessing the software and computing needs of a particular project.

The first step consists of answering the following questions:

• In a paragraph, describe what is the project about.
• List the project's specific goals (e.g. make the method available for public use, create a web service, present this analysis)
• Think about what are your computing/software needs, and list them.

Once a general overview of the project has been defined, the next step consists of analyzing the following:

R packages development

Fundamental questions/tasks

• Check for other R packages/software that does what the project tries to do.
• Describe the ultimate goal of your R package (e.g. solve an optim problem, implement a visualization problem, estimate parameters, etc.)
• Think about data (if any needed), in particular, input/output, have you checked any R packages that already have this?
• Create a repository for the package.

Once the project is on git, following checkmarks

• The package uses roxygen2https://urldefense.com/v3/__https://cran.r-project.org/package=roxygen2__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMcO0jZ-t$ (you can turn your package Rd files to roxygen using Rd2roxygenhttps://urldefense.com/v3/__https://cran.r-project.org/package=Rd2roxygen__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMUTekm4Z$).
• The package's functions are thoroughly documented. This includes Description, parameters (@param), value (@return), details (if any), examples (@details), references (@references) and links to other functions (@seealso, and @family).
• The package has been fully tested using testthathttps://urldefense.com/v3/__https://cran.r-project.org/package=testthat__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMVrrtcoy$ or another framework.
• The project is built using Continuous Integration services as Travis-cihttps://urldefense.com/v3/__https://travis-ci.org__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMQTBO0hl$ and Appveyorhttps://urldefense.com/v3/__https://ci.appveyor.com/__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMU98hath$ (use the usethishttps://urldefense.com/v3/__http://usethis.r-lib.org/__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMSnjgOxP$ package to set it up, eg: usethis::use_travis).
• The package includes a vignette with an extended example and, if needed, references on the package.
• The package has a website (suggest using pkgdownhttps://urldefense.com/v3/__https://pkgdown.r-lib.org__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMZOI2EMI$)

Sending a package to CRAN

Prepare for release:

• devtools::check_win_devel()
• rhub::check_for_cran()
• revdepcheck::revdep_check(num_workers = 4)
• Polish NEWShttps://urldefense.com/v3/__http://style.tidyverse.org/news.html*before-release__;Iw!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMdmyQPHt$
• If new failures, update email.yml then revdepcheck::revdep_email_maintainers()

Perform release:

• Bump version (in DESCRIPTION and NEWS)
• devtools::check_win_devel() (again!)
• devtools::submit_cran()
• pkgdown::build_site()
• Approve email

Wait for CRAN...

• Tag release
• Bump dev version

Sending a package to Bioconductor

Prepare for release:

• Pass R CMD check and R CMD Biocheck
• Go visit this guidance sitehttps://urldefense.com/v3/__https://github.com/Bioconductor/Contributions__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMfkiNp8H$
• Add SSH public key(s) to your GitHub account
• Add a webhook to your repository
• Submit by opening a new issue in the Bioconductor Contributionshttps://urldefense.com/v3/__https://github.com/Bioconductor/Contributions/issues/new__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMYbsh4WT$ repository.

Perform release:

• Bump version (in DESCRIPTION and NEWS) which triggers the submission
• Receive emails about successfully building your package without errors or warnings.
• A technical review provided by a Bioconductor team member
• Approve email

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/USCbiostats/AnnoQR/issues/1__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMW-8eGym$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ACSAG7LDQRVY64RU5MEBC5DSITX3LANCNFSM4SA6R6UA__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMezAH22w$.