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Bioconductor Packages: Development, Maintenance, and Peer Review

Table of contents

  • Welcome
  • Package Submissions
  • Overview
  • 1 Bioconductor Package Submissions
  • Package Development Guidelines
  • Overview
  • 2 Package name
  • 3 General Bioconductor Package Development
  • 4 Important Bioconductor Package Development Features
  • 5 The README file
  • 6 The DESCRIPTION file
  • 7 The NAMESPACE file
  • 8 The NEWS file
  • 9 The LICENSE file
  • 10 The CITATION file
  • 11 The INSTALL file
  • 12 Documentation
  • 13 Package data
  • 14 Unit tests
  • 15 R code
  • 16 Fortran / C / C++ / Python / Third-Party Code
  • 17 Shiny apps
  • 18 Non-Software Packages
  • 19 The .gitignore file
  • 20 Conclusion
  • Bioconductor Package Maintenance
  • Overview
  • 21 Git Version Control
  • 22 Version Numbering
  • 23 Troubleshooting Build Report
  • 24 Debugging C/C++ code
  • 25 Deprecation Guidelines
  • 26 Package End of Life Policy
  • 27 Branch Rename FAQs
  • Package Reviewer Resources
  • Overview
  • 28 Review Expectations
  • 29 Reviewer Resources and Tools
  • 30 Volunteer to Review
  • Appendix
  • A Using the ‘Devel’ Version of Bioconductor
  • B Long Tests
  • C Querying Web Resources
  • D C and Fortran code
  • E C++/Mavericks Best Practices
  • F Debug: Links in Rd files
  • G NEWS

View book source

F Debug: Links in Rd files

F.1 Context

This chapter describes an issue resolved on 31-May-2022.

The objective was to include a link from the man page of one package to the man page of the SummarizedExperiment class in the SummarizedExperiment package.

Using roxygen2, the link was written as follows in the R file:

#' ... \linkS4class{SummarizedExperiment} ...

The issue was that rcmdcheck::rcmdcheck() reported the following WARNING:

W  checking Rd cross-references (<...>ms)
   Missing link or links in documentation object '<...>.Rd':
     ‘SummarizedExperiment-class’
   
   See section 'Cross-references' in the 'Writing R Extensions' manual.

F.2 What worked

First, the SummarizedExperiment package was added to the Depends: section of the DESCRIPTION file.

Depends:
    SummarizedExperiment

At that point, rcmdcheck::rcmdcheck() dropped the previous WARNING and instead displayed the following NOTE.

N  checking dependencies in R code (7.9s)
   Package in Depends field not imported from: ‘SummarizedExperiment’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.

Then, the following line was added to the R script.

#' @import SummarizedExperiment

Next, devtools::document() was run, adding the following line to the NAMESPACE file.

import(SummarizedExperiment)

At which point rcmdcheck::rcmdcheck() did not return any more issue.

F.3 What did not work

Adding the SummarizedExperiment package to the Imports: section of the DESCRIPTION file, adding an @import statement in the documentation, and running devtools::document(). At that point, rcmdcheck::rcmdcheck() continued to display the initial WARNING.

F.4 Additional resources

  • Rd formatting
E C++/Mavericks Best Practices
G NEWS

On this page

  • F Debug: Links in Rd files
  • F.1 Context
  • F.2 What worked
  • F.3 What did not work
  • F.4 Additional resources
  • View source
  • Edit this page

"Bioconductor Packages: Development, Maintenance, and Peer Review" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-04-09.

This book was built by the bookdown R package.