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Fix {.topic} to use required pkg::topic format with display text

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{.topic} in cli requires a package-qualified topic reference to generate
a valid x-r-help:pkg::topic URI. Bare {.topic AMR-options} produced a
malformed x-r-help:AMR-options URI (no package prefix).

Use the [display_text](pkg::topic) form throughout:
  {.topic [AMR-options](AMR::AMR-options)}
  {.topic [AMR-deprecated](AMR::AMR-deprecated)}

The hyphen in the topic name is fine as a URI string even though
AMR::AMR-options is not a valid R symbol expression.

The fallback handler in format_message() already handles the [text](uri)
form by extracting the display text, so plain-text output is unchanged.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 22:47:38 +00:00
parent 8760c6d85a
commit 5ecbc9001e
4 changed files with 6 additions and 6 deletions
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2
R/interpretive_rules.R
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@@ -1097,7 +1097,7 @@ eucast_rules <- function(x,
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
...) {
if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic AMR-options}.")
warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic [AMR-options](AMR::AMR-options)}.")
}
interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
}