Package Submission

Introduction

Bioconductor Packages should

Bioconductor Authors should

Other avenues for distributing your package include

Many Bioconductor packages import or depend on CRAN packages. CRAN packages importing or depending on many Bioconductor packages can be problematic, because of the different approaches to repository structure and release schedules.

Your package cannot depend on any package (or version of a package) that is not (yet) available on CRAN or Bioconductor.

Checklist

Packages must satisfy the following checklist:

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Submission

Note - your DESCRIPTION file will be automatically attached the issue you create, as a convenient summary of your package.

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.).

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.

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.

Review Process

After you submit a GitHub repository, a human will intervene to allow the package to build. A reviewer will be automatically assigned. Then a comment will be posted to the issue you created, with the result of R CMD build, R CMD check and R CMD BiocCheck on all three platforms. Please address all the Warnings from R CMD check and all ‘Required’ and ‘Recommended’ issues from R CMD BiocCheck. 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.

A typical review works as follows.

Following acceptance of a package:

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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.

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Source Code & Build Reports »

Source code is stored in svn (user: readonly, pass: readonly).

Software packages are built and checked nightly. Build reports:

 

Development Version »

Bioconductor packages under development:

Developer Resources: