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Fix namespace load failure: remove assignInNamespace from .onLoad (#268)

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assignInNamespace cannot add NEW bindings to a locked package namespace
(R locks namespace bindings before .onLoad runs). Replace the .onLoad
shim with a runtime fallback inside interpretive_rules(): if
INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive
it from EUCAST_RULES_DF by adding the rule.provider column. This also
fixes the screening_abx line to reuse the already-resolved
interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF
reference.

https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
This commit is contained in:
Claude
2026-05-01 06:19:17 +00:00
parent befbccc304
commit 7c945b8081
2 changed files with 12 additions and 14 deletions
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15
R/interpretive_rules.R
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@@ -619,9 +619,18 @@ interpretive_rules <- function(x,
} else if (!is.null(list(...)$eucast_rules_df)) {
# deprecated parameter name kept for backward compatibility
interpretive_rules_df_total <- list(...)$eucast_rules_df
} else {
# otherwise internal data file, created in data-raw/_pre_commit_checks.R
} else if (exists("INTERPRETIVE_RULES_DF", envir = asNamespace("AMR"), inherits = FALSE)) {
# internal data file, created in data-raw/_pre_commit_checks.R
interpretive_rules_df_total <- INTERPRETIVE_RULES_DF
} else {
# transitional fallback: sysdata.rda predates the rename from EUCAST_RULES_DF
# re-run data-raw/_pre_commit_checks.R to regenerate sysdata.rda
interpretive_rules_df_total <- EUCAST_RULES_DF
interpretive_rules_df_total$rule.provider <- "EUCAST"
interpretive_rules_df_total <- interpretive_rules_df_total[
, c("rule.provider", setdiff(colnames(interpretive_rules_df_total), "rule.provider")),
drop = FALSE
]
}
## filter on guideline provider and user-set guideline versions ----
@@ -661,7 +670,7 @@ interpretive_rules <- function(x,
# sometimes, the screenings are missing but the names are actually available
# we only hints on remaining rows in `interpretive_rules_df`
screening_abx <- as.character(AMR::antimicrobials$ab[which(AMR::antimicrobials$ab %like% "-S$")])
screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(INTERPRETIVE_RULES_DF$and_these_antibiotics[!is.na(INTERPRETIVE_RULES_DF$and_these_antibiotics)], ", *")))]
screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(interpretive_rules_df_total$and_these_antibiotics[!is.na(interpretive_rules_df_total$and_these_antibiotics)], ", *")))]
if (isTRUE(info)) {
cat("\n")
}

11
R/zzz.R
View File

@@ -112,17 +112,6 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
AMR_env$AB_lookup <- cbind(AMR::antimicrobials, AB_LOOKUP)
AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
# Transitional: create INTERPRETIVE_RULES_DF alias if sysdata.rda predates the rename from EUCAST_RULES_DF.
# Remove this block once data-raw/_pre_commit_checks.R has been re-run.
ns <- asNamespace("AMR")
if (!exists("INTERPRETIVE_RULES_DF", envir = ns, inherits = FALSE) &&
exists("EUCAST_RULES_DF", envir = ns, inherits = FALSE)) {
df <- get("EUCAST_RULES_DF", envir = ns)
df$rule.provider <- "EUCAST"
df <- df[, c("rule.provider", setdiff(colnames(df), "rule.provider")), drop = FALSE]
assignInNamespace("INTERPRETIVE_RULES_DF", df, ns = "AMR")
}
}
.onAttach <- function(libname, pkgname) {