From 7c945b80819f8452aa64c57dc85f43b8f9d81536 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Fri, 1 May 2026 06:19:17 +0000
Subject: [PATCH] Fix namespace load failure: remove assignInNamespace from
 .onLoad (#268)

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
---
 R/interpretive_rules.R | 15 ++++++++++++---
 R/zzz.R                | 11 -----------
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/R/interpretive_rules.R b/R/interpretive_rules.R
index a91e222a2..7e57bb5a6 100755
--- a/R/interpretive_rules.R
+++ b/R/interpretive_rules.R
@@ -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$and_these_antibiotics)], ", *")))]
   if (isTRUE(info)) {
     cat("\n")
   }
diff --git a/R/zzz.R b/R/zzz.R
index 5417b2ea9..39eca912f 100755
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -112,17 +112,6 @@ AMR_env$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) {