Package Submission

This page gives an overview of the submission process along with key principles to follow. See also Package Guidelines for package specific guidelines and requirement and the Bioconductor new package submission tracker.

• Introduction
• Types of Packages
• Author/Maintainer Expectations
• Submission
• Experiment data package
• Annotation package
• Review Process
• Following Acceptance
• Additional Support

Introduction

To submit a package to Bioconductor the package should:

• Address areas of high-throughput genomic analysis, e.g., sequencing, expression and other microarrays, flow cytometry, mass spectrometry, image analysis; see biocViews.
• Interoperate with other Bioconductor packages by re-using common data structures (see S4 classes and methods) and existing infrastructure (e.g., rtracklayer::import() for input of common genomic files).
• Adopt software best practices that enable reproducible research and use, such as full documentation and vignettes (including fully evaluated code) as well as commitment to long-term user support through the Bioconductor support site.
• Not exist on CRAN. A package can only be submitted to one or the other.
• Comply with Package Guidelines.
• Your package cannot depend on any package (or version of a package) that is not (yet) available on CRAN or Bioconductor.

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Types of Packages

Bioconductor packages are broadly defined by three main package types: Software, Experiment Data, and Annotation.

• Most packages contributed by users are software packages. Software packages provide implementation of algorithms (e.g. statistical analysis), access to resources (e.g. biomart, or NCBI) or visualizations (e.g. volcano plots, pathways plots). Instructions for creating Software packages can be found here: Package guidelines.

• Annotation packages are database-like packages that provide information linking identifiers (e.g., Entrez gene names or Affymetrix probe ids) to other information (e.g., chromosomal location, Gene Ontology category). It is also encouraged to utilize AnnotationHub for storage and access to large raw data files and their conversion to standard R formats. Instructions for adding data to AnnotationHub and designing a annotation package to use AnnotationHub can be found here: Creating AnnotationHub Packages.

• Experiment data packages provide data sets that are used, often by software packages, to illustrate particular analyses. These packages contain curated data from an experiment, teaching course or publication and in most cases contain a single data set. It is also encouraged to utilize ExperimentHub for storage and access to larger data files. ExperimentHub is also particularly useful for hosting collections of related data sets. Instructions for adding data to ExperimentHub and designing an experiment data package to use ExperimentHub can be found here: Creating ExperimentHub Packages.

See Package Guidelines for details on package format and syntax.

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Author / Maintainer Expectations

Acceptance of packages into Bioconductor brings with it ongoing package maintenance responsibilities. Package authors are expected to:

• Follow Bioconductor guidelines

  These include standard guidelines, version numbering, coding style, code performance requirements, memory usage, using existing data classes, and the other requirements described below.

• Follow the release cycle of Bioconductor

  There are two releases each year, around April and October. The release schedule will indicate the timetables and deadlines for each release. A release cycle typically produces two versions of packages, ‘devel’ and ‘release’. It is important to be familiar with these branch concepts. Once your package has been accepted, it will initially be in the ‘devel’ branch. The current devel branch becomes the next release. Most users are expected to use the release branch, so they will not immediately have access to your package until the next release. Bug fixes can be fixed in both branches, while new features should only be added to the ‘devel’ branch.

• Maintain the package using version control

  Realize that Bioconductor, unlike CRAN, maintains all package source code under git version control. This means that you make changes to your package using git. If your package is accepted, you will receive instructions with typical git operations (see the after acceptance section). Package maintenance through software release cycles, including prompt updates to software and documentation, is needed due to possible underlying changes in R and/or other package dependencies.

• Subscribe to the bioc-devel mailing list

  The Bioconductor team communicates with developers through this list. It is also a good channel to communicate changes to other developers. Addressing Bioconductor team requests in a timely manner guarantees that your package remains available through Bioconductor.

• Register on and use the support site

  The support site is the official support channel for users. Users and even developers may ask questions regarding your package on this platform. Be sure to include all the packages that you maintain in the “Watched Tags” section of your support site profile. This will notify you of any questions posted regarding your package(s). It is important to promptly respond to bug reports and questions either on the Bioconductor support site post or directly to developers. Some maintainers prefer to indicate a BugReports: field in their package’s DESCRIPTION file. This field indicates a particular web page for submitting bug reports and questions.

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Submission

• Read and follow the full Contributor Guidelines section and make yourself familiar with the Bioconductor Developer pages.

• Submit by opening a new issue in the Bioconductor Contributions repository, following the guidelines of the README.md file. Assuming that your package is in a GitHub Repository and under the default branch, add the link to your repository to the issue you are opening. You cannot specify any alternative branches; the default branch is utilized. The default branch must contain only package code. Any files or directories for other applications (Github Actions, devtool, etc) should be in a different branch.

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Experiment Data Packages

Experimental data packages contain data specific to a particular analysis or experiment. They often accompany a software package for use in the examples and vignettes and in general are not updated regularly. If you need a general subset of data for workflows or examples first check the AnnotationHub resource for available files (e.g., BAM, FASTA, BigWig, etc.) or ExperimentHub for available processed example data set already included in Bioconductor. If no current files or data sets are appropriate consider an associated Experiment Data Package that utilizes ExperimentHub.

If you have an associated data package for your software package, please do NOT create a separate issue in the our tracker repository for that. Instead, please add the data package repository to the same issue as the software package. The process for doing this is documented here.

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Annotation Packages

Annotation packages contain lightly or non-curated data from a public source and are updated with each Bioconductor release (every 6 months). They are a source of general annotation for one or many organisms and are not specific to a particular experiment. When possible, they should support the select() interface from AnnotationDbi.

Annotation packages should NOT be posted to the tracker repository. Instead send an email to packages@bioconductor.org with a description of the proposed annotation package and futher instructions of where to send the package will be provided. Whenever possible Annotation Packages should use the AnnotationHub for managing files.

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Review Process

• A new package is initially labeled as ‘1. 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 re-labelled ‘2. review in progress’ and a reviewer will be automatically assigned. Your assigned reviewer will address your concerns and help you through the review process. The entire review process typically takes between 2 and 5 weeks.

• The package will be submitted to the Bioconductor build system (BBS). The system will check out your package from GitHub. It will then run R CMD build to create a ‘tarball’ of your source code, vignettes, and man pages. It 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 will perform these steps using the ‘devel’ version of Bioconductor, on three platforms (Linux, Mac OS X, and Windows). After these steps are complete, a link to a build report will be appended to the new package issue. 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 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. Pre-release versions utilize the 0.99.z format. When accepted and released, your package’s version number will be automatically incremented to 1.0.0.

• 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 Git repository and to the 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 Server.

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Following Acceptance

Following acceptance of a package:

• Packages accepted on the tracker repository are added to the ‘devel’ branch of the Bioconductor GIT repository, with the current version number of the accepted package.
• Packages are then built by the Bioconductor nightly build process. If the build is successful, the package has its own ‘landing page’ created, and the package is made available to users of the ‘devel’ branch of Bioconductor via BiocManager::install().
• Changes to their package (if any), should be done to version in the Bioconductor git server.

• Developers should bump the z portion of their version number every time they commit changes to their package, following the Version numbering guidelines. If developers don’t bump the version, the changes made to their package do not propagate to the Bioconductor web site and package repository.

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Additional Support

We are eager to enhance the quality and interoperability of Bioconductor software and will provide additional support when requested by package developers. Example areas of assistance include use of appropriate S4 structures, specific guidance on efficient implementation, guidance on code structure, and critical assessment of package documentation and structure. Use the bioc-devel mailing list or email packages@bioconductor.org to obtain additional support.

• Support Email: packages@bioconductor.org

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