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:
SummarizedExperimentAt 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 SummarizedExperimentNext, 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.