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 <[email protected]> Sent: Thursday, October 1, 2020 2:27 PM To: USCbiostats/AnnoQR <[email protected]> Cc: Subscribed <[email protected]> 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 roxygen2<https://urldefense.com/v3/__https://cran.r-project.org/package=roxygen2__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMcO0jZ-t$> (you can turn your package Rd files to roxygen using Rd2roxygen<https://urldefense.com/v3/__https://cran.r-project.org/package=Rd2roxygen__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMUTekm4Z$>). * 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 testthat<https://urldefense.com/v3/__https://cran.r-project.org/package=testthat__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMVrrtcoy$> or another framework. * The project is built using Continuous Integration services as Travis-ci<https://urldefense.com/v3/__https://travis-ci.org__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMQTBO0hl$> and Appveyor<https://urldefense.com/v3/__https://ci.appveyor.com/__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMU98hath$> (use the usethis<https://urldefense.com/v3/__http://usethis.r-lib.org/__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMSnjgOxP$> 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 pkgdown<https://urldefense.com/v3/__https://pkgdown.r-lib.org__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMZOI2EMI$>) Sending a package to CRAN Prepare for release: * devtools::check_win_devel() * rhub::check_for_cran() * revdepcheck::revdep_check(num_workers = 4) * Polish NEWS<https://urldefense.com/v3/__http://style.tidyverse.org/news.html*before-release__;Iw!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMdmyQPHt$> * 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 site<https://urldefense.com/v3/__https://github.com/Bioconductor/Contributions__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMfkiNp8H$> * Add SSH public key(s) to your GitHub account * Add a webhook to your repository * Submit by opening a new issue in the Bioconductor Contributions<https://urldefense.com/v3/__https://github.com/Bioconductor/Contributions/issues/new__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMYbsh4WT$> 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 GitHub<https://urldefense.com/v3/__https://github.com/USCbiostats/AnnoQR/issues/1__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMW-8eGym$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ACSAG7LDQRVY64RU5MEBC5DSITX3LANCNFSM4SA6R6UA__;!!LIr3w8kk_Xxm!59eHkWapl7M3hKjWCDz_ToqqCqYE-E2Q8RyM7pWBcyhYU5mGY_-VMezAH22w$>.