7 The NAMESPACE file

A NAMESPACE file defines the functions, classes, and methods that are imported into the namespace, and exported for users.

In the following section we describe what Bioconductor reviewers will be looking for in this file.

7.1 Function names

Exported functions should use camel case or underscoring and not include ., which indicates S3 dispatch. Functions starting with . should not be exported as that indicates an internal function.

7.2 Imported functions

Generally importFrom() is encouraged over importing an entire package. However, if there are many functions from a single package, import() can be acceptable. If a particular Bioconductor class is used or extended it is highly recommended to import() the full package so that full class functionality is inherited automatically; there are exceptions depending on implementation and necessity.

7.3 Exported functions

Exporting all functions with exportPattern("^[[:alpha:]]+") is strongly discouraged and almost always not allowed. Functions and generics should be exported individually, for clarity and control.