Consider contributing your completed R package to Bioconductor if the
- Addresses areas of high-throughput genomic analysis where
Bioconductor already makes significant contributions, e.g.,
sequencing, expression and other microarrays, flow cytometry, mass
spectrometry, image analysis; see
- Interoperates with other Bioconductor packages, re-using common data
S4 classes and methods) and
existing infrastructure (e.g.,
rtracklayer::import() for input of
common genomic files).
- Adopts 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
Other avenues for distributing your package include
CRAN (for packages only tangentially
related to areas of Bioconductor emphasis) and repositories such as
github (for packages in early stages of
development). 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.
Packages submitted to Bioconductor must meet a checklist
of standards of functionality, documentation, and
interoperability. See Contact information to obtain
instructions for submitting new packages.
Authors receive initial feedback in 1 to 3 weeks. Packages will be checked
for adherence to the Bioconductor package guidelines and the checklist below
by a member of Bioconductor team. Package developers should consult the full
Bioconductor Package Guidelines. Submission
implies commitment to package maintenance across multiple release cycles.
Packages must satisfy the following checklist:
R CMD build,
R CMD check, and
R CMD BiocCheck (see the
R CMD check
cheatsheet and the BiocCheck package) on all supported platforms (Windows, Macintosh, Linux)
with no errors or warnings, using a recent R-devel.
The result of
R CMD build must be less than 4MB;
R CMD check must complete within 5 minutes.
- Contain a DESCRIPTION file with valid contact information, an informative
title and description, correct license specification, appropriate biocViews
terms, valid version number.
- Set Version: 0.99.0 in the DESCRIPTION. Subsequent versions created
during the review process will be numbered 0.99.1, 0.99.2, etc.
When released, your package’s version number will be automatically
incremented to 1.0.0.
- Contain a NAMESPACE that imports all symbols used in the package, and
exports just those symbols the package author identifies as appropriate.
Use of a NAMESPACE implies that appropriate packages are mentioned in the
Imports: field of the DESCRIPTION file.
- Contain a Sweave-style vignette that illustrates the major uses of the
package. The vignette must be evaluated during package installation; a
static vignette (e.g., PDF) is not acceptable.
- Contain complete help pages. This includes accurate description of function
parameter and return values, and meaningful examples.
- Make use of appropriate existing packages (e.g., biomaRt, AnnotationDbi,
Biostrings) and classes (e.g., ExpressionSet, AnnotatedDataFrame,
RangedData, Rle, DNAStringSet) to avoid duplication of functionality
available in other Bioconductor packages.
- Contain no extraneous files (e.g., ‘.DS_Store’, ‘.project’, ‘.svn’, etc.),
files with invalid names (e.g., differing only in case), or code that
cannot be distributed under the license specified by the author.
- Packages must not already be available on CRAN.
- Packages should have a descriptive name that is not already in use.
See if it is by running
cannot have a package name that is case-insensitively equal to
an existing package name in CRAN or Bioconductor.
Packages should also conform to the following:
- Use existing S4 classes and generic functions; see the
Package Guidelines for details on
- Include an inst/NEWS file for providing users with information on package
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From submission to acceptance
- Package developers submit their first version of a package with the
version number at 0.99.0
- A detailed package review is returned to the developer
- The package developer updates their package, increments the version
number to 0.99.1, builds and checks the package on the local
machine, and re-submitts the package to Bioconductor.
- The process is repeated, with version bumps on each iteration, until
the package is accepted to Bioconductor.
- A package was submitted as ‘DemoPackage_0.99.0.tar.gz’
- During package review it was recommended that biocViews terms in the
DESCRIPTION file, a NEWS file and a vignette be added.
- The package developer made all the recommended changes, bumped the
version number to 0.99.1 in the DESCRIPTION file, built and checked
the package on their local machine.
- The developer uploaded the tar ball ‘DemoPackage_0.99.1.tar.gz’ to
Following acceptance of a package:
- Packages accepted on the tracker are added to the devel branch of
the Bioconductor SVN 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
- Developers may continue to make changes to their package, but now do
so to the version in the subversion repository.
- 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
If the developer had made an error and not bumped the version from
0.99.1 to 0.99.2, then the package would be built by the nightly build
process, but the new version would not propagate to the public
biocLite("DemoPackage") would return the old version
0.99.1 of the package.
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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 the Contact
information below to obtain additional support.
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To submit a package or obtain additional support, contact Sonali Arora
(email: packages NEAR bioconductor POINT org)
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