diff --git a/R/qenv-join.R b/R/qenv-join.R
index 1d214bf4f..f644223a0 100644
--- a/R/qenv-join.R
+++ b/R/qenv-join.R
@@ -7,102 +7,101 @@
 #' See below for an example.
 #'
 #' There are some situations where `join()` cannot be properly performed, such as these three scenarios:
-#' \enumerate{
-#'   \item Both `qenv` objects contain an object of the same name but are not identical. \cr\cr
-#'   Example:
-#'   \preformatted{
-#'   x <- qenv(
-#'     code = c(mtcars1 = "mtcars1 <- mtcars"),
-#'     env = list2env(list(mtcars1 = mtcars))
-#'   )
-#'   y <- qenv(
-#'     code = c(mtcars1 = "mtcars1 <- mtcars['wt']"),
-#'     env = list2env(list(mtcars1 = mtcars['wt']))
-#'   )
-#'   z <- join(x, y)
-#'   # Error message will occur
-#'   }
-#'   In this example, `mtcars1` object exists in both `x` and `y` objects but the content are not identical.\cr
-#'   `mtcars1` in the `x qenv` object has more columns than `mtcars1` in the `y qenv` object (only has one column).
-#'   \item `join()` will look for identical `@id` values in both `qenv` objects.
-#'   The index position of these `@id`s must be the same to determine the evaluation order.
-#'   Otherwise, `join()` will throw an error message.\cr\cr
-#'   Example:
-#'   \preformatted{
-#'   common_q <- qenv(code = "v <- 1", env = list2env(list(v = 1)))
-#'   x <- eval_code(
-#'     common_q,
-#'     "x <- v"
-#'   )
-#'   y <- eval_code(
-#'     common_q,
-#'     "y <- v"
-#'   )
-#'   z <- eval_code(
-#'     y,
-#'     "z <- v"
-#'   )
-#'   q <- join(x, y)
-#'   join_q <- join(q, z)
-#'   # Error message will occur
-#'
-#'   # Check the order of evaluation based on the id slot
-#'   shared_ids <- intersect(q@id, z@id)
-#'   match(shared_ids, q@id) # Output: 1 3
-#'   match(shared_ids, z@id) # Output: 1 2
-#'   }
-#'   The error occurs because the index position of identical `@id` between the two objects is not the same.
-#'   \item The usage of temporary variable in the code expression could cause `join()` to fail. \cr\cr
-#'   Example:
-#'   \preformatted{
-#'   common_q <- qenv()
-#'   x <- eval_code(
-#'     common_q,
-#'     "x <- numeric(0)
-#'      for (i in 1:2) {
-#'        x <- c(x, i)
-#'      }"
-#'   )
-#'   y <- eval_code(
-#'     common_q,
-#'     "y <- numeric(0)
-#'      for (i in 1:3) {
-#'        y <- c(y, i)
-#'      }"
-#'   )
-#'   q <- join(x,y)
-#'   # Error message will occur
-#'
-#'   # Check the value of temporary variable i in both objects
-#'   x@env$i # Output: 2
-#'   y@env$i # Output: 3
-#'   }
-#'   `join()` fails to provide a proper result because of the temporary variable `i` exists
-#'   in both objects but has different value.\cr
-#'   To fix this, we can set `i <- NULL` in the code expression for both objects.
-#'   \preformatted{
-#'   common_q <- qenv()
-#'   x <- eval_code(
-#'     common_q,
-#'     "x <- numeric(0)
-#'      for (i in 1:2) {
-#'        x <- c(x, i)
-#'      }
-#'      # dummy i variable to fix it
-#'      i <- NULL"
-#'   )
-#'   y <- eval_code(
-#'     common_q,
-#'     "y <- numeric(0)
-#'      for (i in 1:3) {
-#'        y <- c(y, i)
-#'      }
-#'      # dummy i variable to fix it
-#'      i <- NULL"
-#'   )
-#'   q <- join(x,y)
-#'   }
-#' }
+#' 1. Both `qenv` objects contain an object of the same name but are not identical.
+#'
+#'    Example:
+#'
+#'    ```r
+#'    x <- eval_code(qenv(), expression(mtcars1 <- mtcars))
+#'    y <- eval_code(qenv(), expression(mtcars1 <- mtcars['wt']))
+#'
+#'    z <- join(x, y)
+#'    # Error message will occur
+#'    ```
+#'    In this example, `mtcars1` object exists in both `x` and `y` objects but the content are not identical.
+#'    `mtcars1` in the `x qenv` object has more columns than `mtcars1` in the `y qenv` object (only has one column).
+#'
+#' 2. `join()` will look for identical `@id` values in both `qenv` objects.
+#'    The index position of these `@id`s must be the same to determine the evaluation order.
+#'    Otherwise, `join()` will throw an error message.
+#'
+#'    Example:
+#'    ```r
+#'    common_q <- eval_code(qenv(), expression(v <- 1))
+#'    x <- eval_code(
+#'      common_q,
+#'      "x <- v"
+#'    )
+#'    y <- eval_code(
+#'      common_q,
+#'      "y <- v"
+#'    )
+#'    z <- eval_code(
+#'      y,
+#'      "z <- v"
+#'    )
+#'    q <- join(x, y)
+#'    join_q <- join(q, z)
+#'    # Error message will occur
+#'
+#'    # Check the order of evaluation based on the id slot
+#'    shared_ids <- intersect(q@id, z@id)
+#'    match(shared_ids, q@id) # Output: 1 3
+#'    match(shared_ids, z@id) # Output: 1 2
+#'    ```
+#'    The error occurs because the index position of identical `@id` between the two objects is not the same.
+#'
+#' 3. The usage of temporary variable in the code expression could cause `join()` to fail.
+#'
+#'    Example:
+#'    ```r
+#'    common_q <- qenv()
+#'    x <- eval_code(
+#'      common_q,
+#'      "x <- numeric(0)
+#'       for (i in 1:2) {
+#'         x <- c(x, i)
+#'       }"
+#'    )
+#'    y <- eval_code(
+#'      common_q,
+#'      "y <- numeric(0)
+#'       for (i in 1:3) {
+#'         y <- c(y, i)
+#'       }"
+#'    )
+#'    q <- join(x,y)
+#'    # Error message will occur
+#'
+#'    # Check the value of temporary variable i in both objects
+#'    x@env$i # Output: 2
+#'    y@env$i # Output: 3
+#'    ```
+#'    `join()` fails to provide a proper result because of the temporary variable `i` exists
+#'    in both objects but has different value.
+#'    To fix this, we can set `i <- NULL` in the code expression for both objects.
+#'    ```r
+#'    common_q <- qenv()
+#'    x <- eval_code(
+#'      common_q,
+#'      "x <- numeric(0)
+#'       for (i in 1:2) {
+#'         x <- c(x, i)
+#'       }
+#'       # dummy i variable to fix it
+#'       i <- NULL"
+#'    )
+#'    y <- eval_code(
+#'      common_q,
+#'      "y <- numeric(0)
+#'       for (i in 1:3) {
+#'         y <- c(y, i)
+#'       }
+#'       # dummy i variable to fix it
+#'       i <- NULL"
+#'    )
+#'    q <- join(x,y)
+#'    ```
 #'
 #' @param x (`qenv`)
 #' @param y (`qenv`)
@@ -167,7 +166,7 @@ setMethod("join", signature = c("qenv.error", "ANY"), function(x, y) {
 #' If two `qenv` can be joined
 #'
 #' Checks if two `qenv` objects can be combined.
-#' For more information, please see \code{\link{join}}
+#' For more information, please see [`join`]
 #' @param x (`qenv`)
 #' @param y (`qenv`)
 #' @return `TRUE` if able to join or `character` used to print error message.
diff --git a/R/utils.R b/R/utils.R
index 623fb90a6..6866b7752 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,13 +1,13 @@
 #' Suppresses plot display in the IDE by opening a PDF graphics device
 #'
-#' This function opens a PDF graphics device using \code{\link[grDevices]{pdf}} to suppress
+#' This function opens a PDF graphics device using [`grDevices::pdf`] to suppress
 #' the plot display in the IDE. The purpose of this function is to avoid opening graphic devices
 #' directly in the IDE.
 #'
 #' @param x lazy binding which generates the plot(s)
 #'
-#' @details The function uses \code{\link[base]{on.exit}} to ensure that the PDF graphics
-#'          device is closed (using \code{\link[grDevices]{dev.off}}) when the function exits,
+#' @details The function uses [`base::on.exit`] to ensure that the PDF graphics
+#'          device is closed (using [`grDevices::dev.off`]) when the function exits,
 #'          regardless of whether it exits normally or due to an error. This is necessary to
 #'          clean up the graphics device properly and avoid any potential issues.
 #'
diff --git a/man/dev_suppress.Rd b/man/dev_suppress.Rd
index 95ec62e25..5cbea7569 100644
--- a/man/dev_suppress.Rd
+++ b/man/dev_suppress.Rd
@@ -13,13 +13,13 @@ dev_suppress(x)
 No return value, called for side effects.
 }
 \description{
-This function opens a PDF graphics device using \code{\link[grDevices]{pdf}} to suppress
+This function opens a PDF graphics device using \code{\link[grDevices:pdf]{grDevices::pdf}} to suppress
 the plot display in the IDE. The purpose of this function is to avoid opening graphic devices
 directly in the IDE.
 }
 \details{
-The function uses \code{\link[base]{on.exit}} to ensure that the PDF graphics
-device is closed (using \code{\link[grDevices]{dev.off}}) when the function exits,
+The function uses \code{\link[base:on.exit]{base::on.exit}} to ensure that the PDF graphics
+device is closed (using \code{\link[grDevices:dev]{grDevices::dev.off}}) when the function exits,
 regardless of whether it exits normally or due to an error. This is necessary to
 clean up the graphics device properly and avoid any potential issues.
 }
diff --git a/man/join.Rd b/man/join.Rd
index d88808b09..40f60d0c4 100644
--- a/man/join.Rd
+++ b/man/join.Rd
@@ -27,100 +27,101 @@ See below for an example.
 
 There are some situations where \code{join()} cannot be properly performed, such as these three scenarios:
 \enumerate{
-\item Both \code{qenv} objects contain an object of the same name but are not identical. \cr\cr
+\item Both \code{qenv} objects contain an object of the same name but are not identical.
+
 Example:
-\preformatted{
-  x <- qenv(
-    code = c(mtcars1 = "mtcars1 <- mtcars"),
-    env = list2env(list(mtcars1 = mtcars))
-  )
-  y <- qenv(
-    code = c(mtcars1 = "mtcars1 <- mtcars['wt']"),
-    env = list2env(list(mtcars1 = mtcars['wt']))
-  )
-  z <- join(x, y)
-  # Error message will occur
-  }
-In this example, \code{mtcars1} object exists in both \code{x} and \code{y} objects but the content are not identical.\cr
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- eval_code(qenv(), expression(mtcars1 <- mtcars))
+y <- eval_code(qenv(), expression(mtcars1 <- mtcars['wt']))
+
+z <- join(x, y)
+# Error message will occur
+}\if{html}{\out{</div>}}
+
+In this example, \code{mtcars1} object exists in both \code{x} and \code{y} objects but the content are not identical.
 \code{mtcars1} in the \verb{x qenv} object has more columns than \code{mtcars1} in the \verb{y qenv} object (only has one column).
 \item \code{join()} will look for identical \verb{@id} values in both \code{qenv} objects.
 The index position of these \verb{@id}s must be the same to determine the evaluation order.
-Otherwise, \code{join()} will throw an error message.\cr\cr
+Otherwise, \code{join()} will throw an error message.
+
 Example:
-\preformatted{
-  common_q <- qenv(code = "v <- 1", env = list2env(list(v = 1)))
-  x <- eval_code(
-    common_q,
-    "x <- v"
-  )
-  y <- eval_code(
-    common_q,
-    "y <- v"
-  )
-  z <- eval_code(
-    y,
-    "z <- v"
-  )
-  q <- join(x, y)
-  join_q <- join(q, z)
-  # Error message will occur
-
-  # Check the order of evaluation based on the id slot
-  shared_ids <- intersect(q@id, z@id)
-  match(shared_ids, q@id) # Output: 1 3
-  match(shared_ids, z@id) # Output: 1 2
-  }
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{common_q <- eval_code(qenv(), expression(v <- 1))
+x <- eval_code(
+  common_q,
+  "x <- v"
+)
+y <- eval_code(
+  common_q,
+  "y <- v"
+)
+z <- eval_code(
+  y,
+  "z <- v"
+)
+q <- join(x, y)
+join_q <- join(q, z)
+# Error message will occur
+
+# Check the order of evaluation based on the id slot
+shared_ids <- intersect(q@id, z@id)
+match(shared_ids, q@id) # Output: 1 3
+match(shared_ids, z@id) # Output: 1 2
+}\if{html}{\out{</div>}}
+
 The error occurs because the index position of identical \verb{@id} between the two objects is not the same.
-\item The usage of temporary variable in the code expression could cause \code{join()} to fail. \cr\cr
+\item The usage of temporary variable in the code expression could cause \code{join()} to fail.
+
 Example:
-\preformatted{
-  common_q <- qenv()
-  x <- eval_code(
-    common_q,
-    "x <- numeric(0)
-     for (i in 1:2) {
-       x <- c(x, i)
-     }"
-  )
-  y <- eval_code(
-    common_q,
-    "y <- numeric(0)
-     for (i in 1:3) {
-       y <- c(y, i)
-     }"
-  )
-  q <- join(x,y)
-  # Error message will occur
-
-  # Check the value of temporary variable i in both objects
-  x@env$i # Output: 2
-  y@env$i # Output: 3
-  }
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{common_q <- qenv()
+x <- eval_code(
+  common_q,
+  "x <- numeric(0)
+   for (i in 1:2) \{
+     x <- c(x, i)
+   \}"
+)
+y <- eval_code(
+  common_q,
+  "y <- numeric(0)
+   for (i in 1:3) \{
+     y <- c(y, i)
+   \}"
+)
+q <- join(x,y)
+# Error message will occur
+
+# Check the value of temporary variable i in both objects
+x@env$i # Output: 2
+y@env$i # Output: 3
+}\if{html}{\out{</div>}}
+
 \code{join()} fails to provide a proper result because of the temporary variable \code{i} exists
-in both objects but has different value.\cr
+in both objects but has different value.
 To fix this, we can set \code{i <- NULL} in the code expression for both objects.
-\preformatted{
-  common_q <- qenv()
-  x <- eval_code(
-    common_q,
-    "x <- numeric(0)
-     for (i in 1:2) {
-       x <- c(x, i)
-     }
-     # dummy i variable to fix it
-     i <- NULL"
-  )
-  y <- eval_code(
-    common_q,
-    "y <- numeric(0)
-     for (i in 1:3) {
-       y <- c(y, i)
-     }
-     # dummy i variable to fix it
-     i <- NULL"
-  )
-  q <- join(x,y)
-  }
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{common_q <- qenv()
+x <- eval_code(
+  common_q,
+  "x <- numeric(0)
+   for (i in 1:2) \{
+     x <- c(x, i)
+   \}
+   # dummy i variable to fix it
+   i <- NULL"
+)
+y <- eval_code(
+  common_q,
+  "y <- numeric(0)
+   for (i in 1:3) \{
+     y <- c(y, i)
+   \}
+   # dummy i variable to fix it
+   i <- NULL"
+)
+q <- join(x,y)
+}\if{html}{\out{</div>}}
 }
 }
 \examples{