From c7b4eae9b950d350b3f05aac094da5462f4099e6 Mon Sep 17 00:00:00 2001
From: stemangiola <mangiolastefano@gmail.com>
Date: Fri, 13 Dec 2024 15:54:26 +1100
Subject: [PATCH] use a function to drop env

---
 NAMESPACE      |  2 ++
 R/methods.R    | 16 ++++++++--------
 R/methods_SE.R |  7 +++----
 R/utilities.R  | 28 ++++++++++++++++++++++++++++
 4 files changed, 41 insertions(+), 12 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 7c9a52af..01ec53b3 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -155,6 +155,7 @@ importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,flatten_if)
 importFrom(rlang,inform)
+importFrom(rlang,is_quosure)
 importFrom(rlang,is_spliced)
 importFrom(rlang,quo)
 importFrom(rlang,quo_is_missing)
@@ -162,6 +163,7 @@ importFrom(rlang,quo_is_null)
 importFrom(rlang,quo_is_symbol)
 importFrom(rlang,quo_is_symbolic)
 importFrom(rlang,quo_name)
+importFrom(rlang,quo_set_env)
 importFrom(rlang,quo_squash)
 importFrom(rlang,set_names)
 importFrom(scales,extended_breaks)
diff --git a/R/methods.R b/R/methods.R
index c79c3d9f..03dac22d 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -477,10 +477,10 @@ setGeneric("scale_abundance", function(.data,
 
 		# Attach column internals
 		add_tt_columns(
-			!!.sample,
-			!!.transcript,
-			!!.abundance,
-			!!(function(x, v)	enquo(v))(x,!!value_scaled)
+			!!(.sample |> drop_enquo_env()),
+			!!(.transcript |> drop_enquo_env()),
+			!!(.abundance |> drop_enquo_env()),
+			!!(((function(x, v)	enquo(v))(x,!!value_scaled)) |> drop_enquo_env())
 		)
 
 
@@ -698,10 +698,10 @@ setGeneric("quantile_normalise_abundance", function(.data,
 
     # Attach column internals
     add_tt_columns(
-      !!.sample,
-      !!.transcript,
-      !!.abundance,
-      !!(function(x, v)	enquo(v))(x,!!value_scaled)
+      !!(.sample |> drop_enquo_env()),
+      !!(.transcript |> drop_enquo_env()),
+      !!(.abundance |> drop_enquo_env()),
+      !!(((function(x, v)	enquo(v))(x,!!value_scaled)) |> drop_enquo_env())
     )
 
 
diff --git a/R/methods_SE.R b/R/methods_SE.R
index f3e8d1f5..1fe580e4 100755
--- a/R/methods_SE.R
+++ b/R/methods_SE.R
@@ -196,7 +196,7 @@ setMethod("tidybulk", "RangedSummarizedExperiment", .tidybulk_se)
 		memorise_methods_used(c("edger", "tmm")) %>%
 
 		# Attach column internals
-		add_tt_columns(.abundance_scaled = !!(function(x, v)	enquo(v))(x,!!as.symbol(value_scaled)))
+		add_tt_columns(.abundance_scaled = !!(((function(x, v)	enquo(v))(x,!!as.symbol(value_scaled))) |> drop_enquo_env()) )
 
 }
 
@@ -321,7 +321,7 @@ setMethod("scale_abundance",
     memorise_methods_used(c("quantile")) %>%
 
     # Attach column internals
-    add_tt_columns(.abundance_scaled = !!(function(x, v)	enquo(v))(x,!!as.symbol(value_scaled)))
+    add_tt_columns(.abundance_scaled = !!(((function(x, v)	enquo(v))(x,!!as.symbol(value_scaled))) |> drop_enquo_env()) )
 
 }
 
@@ -953,8 +953,7 @@ setMethod("remove_redundancy",
 		memorise_methods_used("sva") %>%
 
 		# Attach column internals
-		add_tt_columns(.abundance_adjusted = !!(function(x, v)
-			enquo(v))(x, !!as.symbol(value_adjusted)))
+	  add_tt_columns(.abundance_adjusted = !!(((function(x, v)	enquo(v))(x,!!as.symbol(value_adjusted))) |> drop_enquo_env()) )
 
 }
 
diff --git a/R/utilities.R b/R/utilities.R
index 3f1dc2bb..c0f9f4e1 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -1514,3 +1514,31 @@ check_and_install_packages <- function(packages) {
     )
   }
 }
+
+#' Drop Environment from a Quosure
+#'
+#' Takes a quosure and resets its environment to `emptyenv()` without altering
+#' its expression.
+#'
+#' @param q A quosure object to have its environment stripped.
+#' @return A quosure with the same expression but environment set to `emptyenv()`.
+#'
+#' @importFrom rlang is_quosure
+#' @importFrom rlang quo_set_env
+#'
+#' @examples
+#' library(rlang)
+#'
+#' q <- quo(x + y)
+#' environment(q)
+#'
+#' q_stripped <- drop_enquo_env(q)
+#' identical(quo_get_env(q_stripped), emptyenv()) # TRUE
+#'
+#' @noRd
+drop_enquo_env <- function(q) {
+  if (!rlang::is_quosure(q)) {
+    stop("`q` must be a quosure.")
+  }
+  rlang::quo_set_env(q, emptyenv())
+}