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Table of Contents

Contributing a Bioconductor Package

This repository is used to contribute new packages to the Bioconductor project for the analysis and comprehension of high-throughput genomic data. Please

By using this service, please note that:

  • Your package code will be visible to the general public, where anyone can see it.

  • The build reports and comments during the review process are public.

  • Any GitHub user may add comments to the package review.

  • You are submitting a package for inclusion in Bioconductor; the build service we provide is meant only for individuals submitting Bioconductor packages.

Starting the Submission Process

To submit a package to Bioconductor:

  1. Create your own GitHub repository, containing source code structured as an R package. The source code must be in a default 'master' branch of your GitHub repository. The master branch must contain only package code.

  2. Add SSH public key(s) to your GitHub account. SSH keys will be used during and after package acceptance for updating the Bioconductor git repository.

  3. Open a new issue. Complete the issue by adding the link to your repository, and confirming that you understand the review process, package guidelines, and maintainer responsibilities. Provide the name of your package as the 'Title' of the issue.

What to Expect

  • A new package is initially labeled as '1a. awaiting moderation'. A Bioconductor team member will take a very brief look at your package, to ensure that it is intended for Bioconductor. Appropriate packages will be labelled '1b. awaiting git addition.

  • The moderator will add your package as a repository to the git.bioconductor.org git server, copy the SSH keys from your github account to the BiocCredentials application, and assign a reviewer. The package will be labelled '2. Review in progress'.

    ALL CHANGES TO YOUR PACKAGE must be pushed to the git.bioconductor.org repository created in this step. See the new package workflow for instructions on pushing changes to your git.bioconductor.org repository.

  • The package will be submitted to the Bioconductor build system. The system will check out your package from git.bioconductor.org.

    The build system will run R CMD build to create a 'tarball' of your source code, vignettes, and man pages.

    The build system will run R CMD check on the tarball, to ensure that the package conforms to standard R programming best practices. Bioconductor has chosen to utilize a custom R CMD check environment; See R CMD check environment for more details.

    Finally, the build system will run BiocCheckGitClone() and BiocCheck() to ensure that the package conforms to Bioconductor BiocCheck standards.

    The system performs these steps using the 'devel' version of Bioconductor, on three platforms (Linux, Mac OS X, and Windows).

  • After the build steps are complete, a link to a build report will be appended to the new package issue on GitHub. Avoid surprises by running these checks on your own computer, under the 'devel' version of Bioconductor, before submitting your package.

  • If the build report indicates problems, modify your package and commit changes to the default branch of your GitHub repository. If there are problems that you do not understand, seek help from your reviewer via a comment on the issue, or on the bioc-devel mailing list.

  • To trigger a new build, include a version bump in your commit, e.g., from Version: 0.99.0 to Version: 0.99.1. Push the changes including version bump to your repository on git.bioconductor.org.

  • Once your package builds and checks without errors or (avoidable) warnings, a Bioconductor team member will provide a technical review of your package. Other Bioconductor developers and users with domain expertise are encouraged to provide additional community commentary. Reviewers will add comments to the issue you created.

  • Respond to the issues raised by the reviewers. You must respond to the primary reviewer, and are strongly encouraged to consider community commentary. Typically your response will involve code modifications; commit these to the default branch of your GitHub repository to trigger subsequent builds. When you have addressed all concerns, add a comment to the issue created in step 2 to explain your response.

  • The reviewer will assess your responses, perhaps suggesting further modifications or clarification. The reviewer will then accept your package for inclusion in Bioconductor, or decline it. The label '2. review in progress' will be replaced by '3a. accepted' or '3b. declined'.

  • If your package is accepted, it will be added to Bioconductor's nightly 'devel' builds. All packages in the 'devel' branch of the repository are 'released' to the user community once every six months, in approximately April and October.

  • Once the review process is complete, the issue you created will be closed. All updates to your package will be through the Bioconductor Git repository.

R CMD check environment

It is possible to activate or deactivate a number of options in R CMD build and R CMD check. Options can be set as individual environment variables or they can be listed in a file. Descriptions of all the different options available can be found here. Bioconductor has chosen to customize some of these options for incoming submission during R CMD check. The file of utilized flags can be downloaded from Github. The file can either be place in a default directory as directed here or can be set through environment variable R_CHECK_ENVIRON with a command similar to

export R_CHECK_ENVIRON = <path to downloaded file>

Submitting Related Packages

Sometimes it is appropriate to contribute more than one package at a time. The most common case is when a software package has a companion experiment data package used for illustrative purposes in the vignette. Remember to avoid circular dependencies between packages.

  1. Start by submitting the package that can be installed without a dependency on any of the other packages you are submitting (this is usually the experiment data package). Do this by creating a new issue as described above.

  2. Continue working with this package until it builds and checks without error on any platform.

    Do not submit an AdditionalPackage with the line shown in step 3 until a review in progress tag has been added to your package and your first package receives a build report

  3. Submit additional packages to the same issue. Do this by posting a comment containing a line like:

     AdditionalPackage: https://github.com/username/repositoryname
    

    Include only one AdditionalPackage line per comment. Wait until this related package has been added to git.bioconductor.org, and it has been updated by you to build successfully before submitting further related packages.

  4. The AdditionalPackage comment must be posted by the same GitHub user who created the issue. Also, the initial package submitted in the issue must have completed the 'moderation' step. If these conditions are not met, the additional package will not build.

  5. The additional package will go through the same preapproval process as described in What to Expect

Circular Dependencies

If circular dependencies are truly unavoidable, there are some subtle differences from the above. Bioconductor will support a 'Suggest / Depend' circular dependency. Most often an accompanied data package will "Suggest" the software package, while the software package will "Depend" on the data package. The single package builder (SPB) handles this case by providing each issue with a unique Rlib path for additional package dependencies. The SPB will install each package before tryng to build or check.

  1. Start by submitting the package with the weaker circular dependency (the package that "Suggests" the other package, most often this will be the data package). Do this by creating a new issue as described above. We will call this package A.

  2. This package A will ERROR when running R CMD build. This is expected since the additional package B would not be found yet.

  3. Submit the additional packages to the same issue. Do this by posting a comment containing a line like:

     AdditionalPackage: https://github.com/username/repositoryname
    
  4. This package B will also ERROR when running R CMD build. This is expected.

  5. Now, perform a version bump on the package A. It should find package B and not ERROR for a missing dependency. Continue working with package A until it builds and checks without error on any platform.

  6. Perform a version bump on package B. It should now find package A and not ERROR for its missing dependency. Continue with the review process.

Additional Actions

To change the repository of your package during the review process:

  1. Edit the first comment in the issue associated with your package. Change the Repository: link to point to your new repository.

  2. Post a comment in your issue, tagging your reviewer, indicating that you have changed the repository.

  3. Once the comment is acknowledged, bump the package version in the new repository to trigger a new build.

To remove an AdditionalPackage: dependency, e.g., because you have identified AnnnotationHub or other resources that make your additional package unnecessary:

  1. Delete or edit all comments with an AdditionalPackage: tag.

Resources

The following pages contain more information about package submission.

If you have a question not answered above, please ask on the bioc-devel mailing list.

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