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