biocthis

[lcolladotor]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/lcolladotor/biocthis

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• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data. Note: it enables creating more packages.

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[bioc-issue-bot]

Hi @lcolladotor

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: biocthis
Title: Automate package and project setup for Bioconductor packages
Version: 0.99.0
Date: 2020-10-01
Authors@R: 
    c(
    person("Leonardo", "Collado-Torres", role = c("aut", "cre"), 
    email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),
    person("Marcel", "Ramos", email = "marcel.ramos@roswellpark.org",
    role = c("ctb"), comment = c(ORCID = "0000-0002-3242-0582"))
    )
Description: This package expands the usethis package with the goal of
    helping automate the process of creating R packages for Bioconductor or
    making them Bioconductor-friendly.
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
URL: https://github.com/lcolladotor/biocthis
BugReports: https://support.bioconductor.org/t/biocthis
biocViews: Software, ReportWriting
Imports: 
    BiocManager,
    fs,
    glue,
    rlang,
    styler,
    usethis
Suggests: 
    BiocStyle,
    covr,
    devtools,
    knitcitations,
    knitr,
    pkgdown,
    rmarkdown,
    sessioninfo,
    testthat,
    utils
VignetteBuilder: knitr

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biocthis to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: e2c538a752b367044adf04a8c9397ec601365f6f

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/biocthis to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[nturaga]

Review

General

I specially enjoyed reading the developer notes for biocthis!

R CMD build

ok

R CMD INSTALL

ok

DESCRIPTION

ok

NAMESPACE

ok

NEWS

ok

actions

• What is the purpose of having the actions directory?

man

ok

vignette

• Very nicely done!

R

• code is clearly written. Good job!

[lcolladotor]

Thanks for the review Nitesh!

I had the actions directory to match what others had done (I think that it was a suggestion by Jim Hester) and it was the original home of the GHA template, but with Marcel Ramos' @LiNk-NY PR, we have deprecated that directory. Currently, it's used by the instructions at https://github.com/r-lib/actions/tree/master/examples#bioconductor-friendly-workflow, particularly

## You can also use this GHA workflow without installing biocthis
usethis::use_github_action(
    "check-bioc",
    "https://bit.ly/biocthis_gha",
    "check-bioc.yml"
)

though https://github.com/lcolladotor/biocthis/blob/master/actions/check-bioc.yml refers to https://github.com/lcolladotor/biocthis/pull/11 and provides instructions for using the new setup.

I could delete the actions directory after sending a PR to r-lib/actions for updating the docs. It might be best to hold off to do this as a single PR once biocthis is part of BioC, to link to the BioC landing page (if this submission is approved).

Best, Leo

[nturaga]

That sounds fair.

Great work @lcolladotor and @LiNk-NY

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/lcolladotor.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("biocthis"). The package 'landing page' will be created at

https://bioconductor.org/packages/biocthis

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.