From 51e46bd2007ea7955849af02b3f41f8b64d41f93 Mon Sep 17 00:00:00 2001
From: m7pr <marcin.kosinski.mk1@roche.com>
Date: Fri, 31 Oct 2025 09:59:33 +0100
Subject: [PATCH 1/9] handle subassignemnts with the same object

---
 R/utils-get_code_dependency.R                 |  16 +-
 .../testthat/test-utils-get_code_dependency.R | 171 ++++++++++++++++++
 2 files changed, 186 insertions(+), 1 deletion(-)

diff --git a/R/utils-get_code_dependency.R b/R/utils-get_code_dependency.R
index 42e0650ad..0690abe92 100644
--- a/R/utils-get_code_dependency.R
+++ b/R/utils-get_code_dependency.R
@@ -306,7 +306,18 @@ extract_occurrence <- function(pd) {
   ans <- move_functions_after_arrow(ans, unique(x[sym_fc_cond, "text"]))
   roll <- in_parenthesis(pd)
   if (length(roll)) {
-    c(setdiff(ans, roll), roll)
+    # detect elements appread in parenthesis and move them on RHS
+    # but only their first appearance
+    # as the same object can appear as regular object and the one used in parenthesis
+    result <- ans
+    for (elem in roll) {
+      idx <- which(result == elem)[1]
+      if (!is.na(idx)) {
+        result <- result[-idx]
+      }
+    }
+    c(result, roll)
+
   } else {
     ans
   }
@@ -330,6 +341,9 @@ move_functions_after_arrow <- function(ans, functions) {
   if (length(arrow_pos) == 0) {
     return(ans)
   }
+  if (length(functions) == 0) {
+    return(ans)
+  }
   before_arrow <- setdiff(ans[1:arrow_pos], functions)
   after_arrow <- ans[(arrow_pos + 1):length(ans)]
   c(before_arrow, unique(c(intersect(ans[1:arrow_pos], functions), after_arrow)))
diff --git a/tests/testthat/test-utils-get_code_dependency.R b/tests/testthat/test-utils-get_code_dependency.R
index 2cd4c40cd..c5b0b272e 100644
--- a/tests/testthat/test-utils-get_code_dependency.R
+++ b/tests/testthat/test-utils-get_code_dependency.R
@@ -86,3 +86,174 @@ testthat::describe("get_code with multiple assignments inside an expression", {
     testthat::expect_equal(get_code(td, names = "var2"), code_source)
   })
 })
+
+testthat::describe("get_code with subassignments", {
+  testthat::it("tracks $ subassignment as producing the base object", {
+    td <- qenv() |>
+      within({
+        iris <- iris
+        iris$Species[sample.int(nrow(iris), 50)] <- NA
+      })
+
+    code_source <- "iris <- iris\niris$Species[sample.int(nrow(iris), 50)] <- NA"
+
+    testthat::expect_equal(get_code(td, names = "iris"), code_source)
+  })
+
+  testthat::it("tracks [ subassignment as producing the base object", {
+    td <- qenv() |>
+      within({
+        x <- 1:10
+        x[1:3] <- c(10, 20, 30)
+      })
+
+    code_source <- "x <- 1:10\nx[1:3] <- c(10, 20, 30)"
+
+    testthat::expect_equal(get_code(td, names = "x"), code_source)
+  })
+
+  testthat::it("tracks [[ subassignment as producing the base object", {
+    td <- qenv() |>
+      within({
+        lst <- list(a = 1, b = 2)
+        lst[["c"]] <- 3
+      })
+
+    code_source <- "lst <- list(a = 1, b = 2)\nlst[[\"c\"]] <- 3"
+
+    testthat::expect_equal(get_code(td, names = "lst"), code_source)
+  })
+
+  testthat::it("tracks nested subassignments", {
+    td <- qenv() |>
+      within({
+        df <- data.frame(x = 1:5, y = 6:10)
+        df$x[df$y > 8] <- 99
+      })
+
+    code_source <- "df <- data.frame(x = 1:5, y = 6:10)\ndf$x[df$y > 8] <- 99"
+
+    testthat::expect_equal(get_code(td, names = "df"), code_source)
+  })
+
+  testthat::it("tracks multiple subassignments to same object", {
+    td <- qenv() |>
+      within({
+        iris <- iris
+        iris$Species[sample.int(nrow(iris), 10)] <- NA
+        iris$Sepal.Length[1:5] <- 0
+      })
+
+    code_source <- "iris <- iris\niris$Species[sample.int(nrow(iris), 10)] <- NA\niris$Sepal.Length[1:5] <- 0"
+
+    testthat::expect_equal(get_code(td, names = "iris"), code_source)
+  })
+
+  testthat::it("tracks subassignments with complex expressions", {
+    td <- qenv() |>
+      within({
+        mat <- matrix(1:12, nrow = 3)
+        mat[mat > 5 & mat < 10] <- 0
+      })
+
+    code_source <- "mat <- matrix(1:12, nrow = 3)\nmat[mat > 5 & mat < 10] <- 0"
+
+    testthat::expect_equal(get_code(td, names = "mat"), code_source)
+  })
+
+  testthat::it("tracks subassignments with function calls on LHS", {
+    td <- qenv() |>
+      within({
+        lst <- list(a = 1, b = 2)
+        names(lst)[1] <- "first"
+      })
+
+    code_source <- "lst <- list(a = 1, b = 2)\nnames(lst)[1] <- \"first\""
+
+    testthat::expect_equal(get_code(td, names = "lst"), code_source)
+  })
+
+  testthat::it("tracks -> operator with subassignments", {
+    td <- qenv() |>
+      within({
+        x <- 1:10
+        c(10, 20, 30) -> x[1:3] # nolint: assignment.
+      })
+
+    code_source <- "x <- 1:10\nx[1:3] <- c(10, 20, 30)"
+
+    testthat::expect_equal(get_code(td, names = "x"), code_source)
+  })
+
+  testthat::it("tracks attributes() function with subassignments", {
+    td <- qenv() |>
+      within({
+        x <- 1:5
+        attributes(x)$names <- letters[1:5]
+      })
+
+    code_source <- "x <- 1:5\nattributes(x)$names <- letters[1:5]"
+
+    testthat::expect_equal(get_code(td, names = "x"), code_source)
+  })
+
+  testthat::it("handles complex nested subassignments", {
+    td <- qenv() |>
+      within({
+        df <- data.frame(x = 1:5, y = 6:10)
+        df[df$x > 2, "y"][1:2] <- c(99, 100)
+      })
+
+    code_source <- "df <- data.frame(x = 1:5, y = 6:10)\ndf[df$x > 2, \"y\"][1:2] <- c(99, 100)"
+
+    testthat::expect_equal(get_code(td, names = "df"), code_source)
+  })
+
+  testthat::it("handles subassignments with multiple operators", {
+    td <- qenv() |>
+      within({
+        lst <- list(a = list(b = 1, c = 2))
+        lst$a$b[2] <- 99
+      })
+
+    code_source <- "lst <- list(a = list(b = 1, c = 2))\nlst$a$b[2] <- 99"
+
+    testthat::expect_equal(get_code(td, names = "lst"), code_source)
+  })
+
+  testthat::it("handles subassignments with data frame column creation", {
+    td <- qenv() |>
+      within({
+        df <- data.frame(x = 1:3)
+        df$new_col <- c("a", "b", "c")
+      })
+
+    code_source <- "df <- data.frame(x = 1:3)\ndf$new_col <- c(\"a\", \"b\", \"c\")"
+
+    testthat::expect_equal(get_code(td, names = "df"), code_source)
+  })
+
+  testthat::it("handles subassignments with matrix indexing", {
+    td <- qenv() |>
+      within({
+        mat <- matrix(1:9, nrow = 3)
+        mat[1:2, 2:3] <- matrix(0, nrow = 2, ncol = 2)
+      })
+
+    code_source <- "mat <- matrix(1:9, nrow = 3)\nmat[1:2, 2:3] <- matrix(0, nrow = 2, ncol = 2)"
+
+    testthat::expect_equal(get_code(td, names = "mat"), code_source)
+  })
+
+  testthat::it("handles subassignments with logical indexing", {
+    td <- qenv() |>
+      within({
+        vec <- 1:10
+        vec[vec %% 2 == 0] <- vec[vec %% 2 == 0] * 2
+      })
+
+    code_source <- "vec <- 1:10\nvec[vec %% 2 == 0] <- vec[vec %% 2 == 0] * 2"
+
+    testthat::expect_equal(get_code(td, names = "vec"), code_source)
+  })
+})

From 9b15b77d759a66409cdfa0bdc36addc06ca21a13 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 31 Oct 2025 09:02:41 +0000
Subject: [PATCH 2/9] [skip style] [skip vbump] Restyle files

---
 R/utils-get_code_dependency.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/utils-get_code_dependency.R b/R/utils-get_code_dependency.R
index 0690abe92..d1cbcbdaf 100644
--- a/R/utils-get_code_dependency.R
+++ b/R/utils-get_code_dependency.R
@@ -317,7 +317,6 @@ extract_occurrence <- function(pd) {
       }
     }
     c(result, roll)
-
   } else {
     ans
   }

From af2fbbb3c57ad929efc165b3d946c663fdeed64c Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 31 Oct 2025 09:05:31 +0000
Subject: [PATCH 3/9] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 74200b457..4b068d46f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -53,7 +53,7 @@ Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate:
     'qenv-c.R'
     'qenv-class.R'

From 24a3f6e78078360bfd689101013ac42cd5226496 Mon Sep 17 00:00:00 2001
From: m7pr <marcin.kosinski.mk1@roche.com>
Date: Fri, 31 Oct 2025 10:19:07 +0100
Subject: [PATCH 4/9] cleanup tests

---
 tests/testthat/test-utils-get_code_dependency.R | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/tests/testthat/test-utils-get_code_dependency.R b/tests/testthat/test-utils-get_code_dependency.R
index c5b0b272e..db06dcdc1 100644
--- a/tests/testthat/test-utils-get_code_dependency.R
+++ b/tests/testthat/test-utils-get_code_dependency.R
@@ -88,18 +88,6 @@ testthat::describe("get_code with multiple assignments inside an expression", {
 })
 
 testthat::describe("get_code with subassignments", {
-  testthat::it("tracks $ subassignment as producing the base object", {
-    td <- qenv() |>
-      within({
-        iris <- iris
-        iris$Species[sample.int(nrow(iris), 50)] <- NA
-      })
-
-    code_source <- "iris <- iris\niris$Species[sample.int(nrow(iris), 50)] <- NA"
-
-    testthat::expect_equal(get_code(td, names = "iris"), code_source)
-  })
-
   testthat::it("tracks [ subassignment as producing the base object", {
     td <- qenv() |>
       within({
@@ -252,7 +240,7 @@ testthat::describe("get_code with subassignments", {
         vec[vec %% 2 == 0] <- vec[vec %% 2 == 0] * 2
       })
 
-    code_source <- "vec <- 1:10\nvec[vec %% 2 == 0] <- vec[vec %% 2 == 0] * 2"
+    code_source <- "vec <- 1:10\nvec[vec%%2 == 0] <- vec[vec%%2 == 0] * 2"
 
     testthat::expect_equal(get_code(td, names = "vec"), code_source)
   })

From 0ba04ccc8f70df177f098ba727d9be6f56839944 Mon Sep 17 00:00:00 2001
From: m7pr <marcin.kosinski.mk1@roche.com>
Date: Fri, 31 Oct 2025 10:48:33 +0100
Subject: [PATCH 5/9] fix move_functions_after_arrow

---
 R/utils-get_code_dependency.R | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/R/utils-get_code_dependency.R b/R/utils-get_code_dependency.R
index d1cbcbdaf..7836ff01b 100644
--- a/R/utils-get_code_dependency.R
+++ b/R/utils-get_code_dependency.R
@@ -343,9 +343,14 @@ move_functions_after_arrow <- function(ans, functions) {
   if (length(functions) == 0) {
     return(ans)
   }
-  before_arrow <- setdiff(ans[1:arrow_pos], functions)
-  after_arrow <- ans[(arrow_pos + 1):length(ans)]
-  c(before_arrow, unique(c(intersect(ans[1:arrow_pos], functions), after_arrow)))
+  ans_pre <- ans[1:arrow_pos]
+  for (fun in functions) {
+    if (any(ans_pre == fun)) ans_pre <- ans_pre[-match(fun, ans_pre)]
+  }
+  after_arrow <- if (arrow_pos < length(ans)) {
+    ans[arrow_pos + 1:length(ans)]
+  }
+  c(ans_pre, after_arrow)
 }
 
 #' Extract side effects

From 98b7597b509293c0582caaaef271ecf239f54d89 Mon Sep 17 00:00:00 2001
From: m7pr <marcin.kosinski.mk1@roche.com>
Date: Fri, 31 Oct 2025 10:57:11 +0100
Subject: [PATCH 6/9] add comments

---
 R/utils-get_code_dependency.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/utils-get_code_dependency.R b/R/utils-get_code_dependency.R
index 7836ff01b..a1ea0b86e 100644
--- a/R/utils-get_code_dependency.R
+++ b/R/utils-get_code_dependency.R
@@ -344,6 +344,10 @@ move_functions_after_arrow <- function(ans, functions) {
     return(ans)
   }
   ans_pre <- ans[1:arrow_pos]
+  # it's setdiff but without the removal of duplicates
+  # do not use setdiff(ans_pre, functions)
+  # as it removes duplicates from ans_pre even if they do not appear in functions
+  # check setdiff(c("A", "A"), "B") - gives "A", where we want to keep c("A", "A")
   for (fun in functions) {
     if (any(ans_pre == fun)) ans_pre <- ans_pre[-match(fun, ans_pre)]
   }

From 2a4a6cf9e632ef5cb7255d3bcd2d730a110326a2 Mon Sep 17 00:00:00 2001
From: Marcin <133694481+m7pr@users.noreply.github.com>
Date: Fri, 31 Oct 2025 11:22:33 +0100
Subject: [PATCH 7/9] Update R/utils-get_code_dependency.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
---
 R/utils-get_code_dependency.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils-get_code_dependency.R b/R/utils-get_code_dependency.R
index a1ea0b86e..237c168a9 100644
--- a/R/utils-get_code_dependency.R
+++ b/R/utils-get_code_dependency.R
@@ -352,7 +352,7 @@ move_functions_after_arrow <- function(ans, functions) {
     if (any(ans_pre == fun)) ans_pre <- ans_pre[-match(fun, ans_pre)]
   }
   after_arrow <- if (arrow_pos < length(ans)) {
-    ans[arrow_pos + 1:length(ans)]
+    ans[(arrow_pos + 1):length(ans)]
   }
   c(ans_pre, after_arrow)
 }

From 7ca59f979263e39487094b389f06c643fc230542 Mon Sep 17 00:00:00 2001
From: Marcin <133694481+m7pr@users.noreply.github.com>
Date: Fri, 31 Oct 2025 11:22:53 +0100
Subject: [PATCH 8/9] Update R/utils-get_code_dependency.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
---
 R/utils-get_code_dependency.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils-get_code_dependency.R b/R/utils-get_code_dependency.R
index 237c168a9..954448d31 100644
--- a/R/utils-get_code_dependency.R
+++ b/R/utils-get_code_dependency.R
@@ -306,7 +306,7 @@ extract_occurrence <- function(pd) {
   ans <- move_functions_after_arrow(ans, unique(x[sym_fc_cond, "text"]))
   roll <- in_parenthesis(pd)
   if (length(roll)) {
-    # detect elements appread in parenthesis and move them on RHS
+    # detect elements appeared in parenthesis and move them on RHS
     # but only their first appearance
     # as the same object can appear as regular object and the one used in parenthesis
     result <- ans

From 3a6ece30e07c944289e3ab901d9d053956a8ea5d Mon Sep 17 00:00:00 2001
From: Marcin <133694481+m7pr@users.noreply.github.com>
Date: Fri, 31 Oct 2025 13:52:01 +0100
Subject: [PATCH 9/9] Apply suggestions from code review

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
---
 .../testthat/test-utils-get_code_dependency.R | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/tests/testthat/test-utils-get_code_dependency.R b/tests/testthat/test-utils-get_code_dependency.R
index db06dcdc1..a9f18f0e8 100644
--- a/tests/testthat/test-utils-get_code_dependency.R
+++ b/tests/testthat/test-utils-get_code_dependency.R
@@ -88,7 +88,7 @@ testthat::describe("get_code with multiple assignments inside an expression", {
 })
 
 testthat::describe("get_code with subassignments", {
-  testthat::it("tracks [ subassignment as producing the base object", {
+  it("tracks [ subassignment as producing the base object", {
     td <- qenv() |>
       within({
         x <- 1:10
@@ -100,7 +100,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "x"), code_source)
   })
 
-  testthat::it("tracks [[ subassignment as producing the base object", {
+  it("tracks [[ subassignment as producing the base object", {
     td <- qenv() |>
       within({
         lst <- list(a = 1, b = 2)
@@ -112,7 +112,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "lst"), code_source)
   })
 
-  testthat::it("tracks nested subassignments", {
+  it("tracks nested subassignments", {
     td <- qenv() |>
       within({
         df <- data.frame(x = 1:5, y = 6:10)
@@ -124,7 +124,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "df"), code_source)
   })
 
-  testthat::it("tracks multiple subassignments to same object", {
+  it("tracks multiple subassignments to same object", {
     td <- qenv() |>
       within({
         iris <- iris
@@ -137,7 +137,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "iris"), code_source)
   })
 
-  testthat::it("tracks subassignments with complex expressions", {
+  it("tracks subassignments with complex expressions", {
     td <- qenv() |>
       within({
         mat <- matrix(1:12, nrow = 3)
@@ -149,7 +149,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "mat"), code_source)
   })
 
-  testthat::it("tracks subassignments with function calls on LHS", {
+  it("tracks subassignments with function calls on LHS", {
     td <- qenv() |>
       within({
         lst <- list(a = 1, b = 2)
@@ -161,7 +161,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "lst"), code_source)
   })
 
-  testthat::it("tracks -> operator with subassignments", {
+  it("tracks -> operator with subassignments", {
     td <- qenv() |>
       within({
         x <- 1:10
@@ -173,7 +173,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "x"), code_source)
   })
 
-  testthat::it("tracks attributes() function with subassignments", {
+  it("tracks attributes() function with subassignments", {
     td <- qenv() |>
       within({
         x <- 1:5
@@ -185,7 +185,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "x"), code_source)
   })
 
-  testthat::it("handles complex nested subassignments", {
+  it("handles complex nested subassignments", {
     td <- qenv() |>
       within({
         df <- data.frame(x = 1:5, y = 6:10)
@@ -197,7 +197,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "df"), code_source)
   })
 
-  testthat::it("handles subassignments with multiple operators", {
+  it("handles subassignments with multiple operators", {
     td <- qenv() |>
       within({
         lst <- list(a = list(b = 1, c = 2))
@@ -209,7 +209,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "lst"), code_source)
   })
 
-  testthat::it("handles subassignments with data frame column creation", {
+  it("handles subassignments with data frame column creation", {
     td <- qenv() |>
       within({
         df <- data.frame(x = 1:3)
@@ -221,7 +221,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "df"), code_source)
   })
 
-  testthat::it("handles subassignments with matrix indexing", {
+  it("handles subassignments with matrix indexing", {
     td <- qenv() |>
       within({
         mat <- matrix(1:9, nrow = 3)
@@ -233,7 +233,7 @@ testthat::describe("get_code with subassignments", {
     testthat::expect_equal(get_code(td, names = "mat"), code_source)
   })
 
-  testthat::it("handles subassignments with logical indexing", {
+  it("handles subassignments with logical indexing", {
     td <- qenv() |>
       within({
         vec <- 1:10