From b24d923ebfae39cfd2888a6942f27e1e3bf880b5 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 15:53:56 +0200
Subject: [PATCH 1/8] refactor: unListDS and replaceNaDS use
 .loadServersideObject

---
 R/replaceNaDS.R                       | 8 +++++---
 R/unListDS.R                          | 9 ++-------
 tests/testthat/test-smk-replaceNaDS.R | 2 +-
 3 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/R/replaceNaDS.R b/R/replaceNaDS.R
index 007e12ce..698fc018 100644
--- a/R/replaceNaDS.R
+++ b/R/replaceNaDS.R
@@ -8,15 +8,17 @@
 #' it might be more sensible to replace all missing values by one specific value e.g. 
 #' replace all missing values in a vector by the mean or median value. Once the missing
 #' values have been replaced a new vector is created.
-#' @param xvect a character, the name of the vector to process.
+#' @param x a character, the name of the vector to process.
 #' @param replacements a vector which contains the replacement value(s), a vector one or 
 #' more values for each study. 
 #' @return a new vector without missing values
 #' @author Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
 #' @export
 #' 
-replaceNaDS <- function(xvect, replacements){
-  
+replaceNaDS <- function(x, replacements){
+
+  xvect <- .loadServersideObject(x)
+
   # check if the input vector is valid (i.e. meets DataSHIELD criteria)
   check <- dsBase::isValidDS(xvect)
   
diff --git a/R/unListDS.R b/R/unListDS.R
index 79e853a8..9b620491 100644
--- a/R/unListDS.R
+++ b/R/unListDS.R
@@ -35,13 +35,8 @@
 #' 
 unListDS <- function(x.name) {
 
-    if (is.character(x.name)) {
-	listvar<-eval(parse(text=x.name), envir = parent.frame())
-    } else {
-        studysideMessage<-"ERROR: x.name must be specified as a character string"
-        stop(studysideMessage, call. = FALSE)
-    } 
- 
+    listvar <- .loadServersideObject(x.name)
+
     outvar<-unlist(listvar)
 
     return(outvar)
diff --git a/tests/testthat/test-smk-replaceNaDS.R b/tests/testthat/test-smk-replaceNaDS.R
index b2b4cfff..8d9c49d7 100644
--- a/tests/testthat/test-smk-replaceNaDS.R
+++ b/tests/testthat/test-smk-replaceNaDS.R
@@ -26,7 +26,7 @@ test_that("simple replaceNaDS", {
     input        <- c(0.0, NA, 2.0, NA, 4.0, NA, 6.0, NA)
     replacements <- c(1.1, 3.3, 5.5, 7.7)
 
-    res <- replaceNaDS(input, replacements)
+    res <- replaceNaDS("input", replacements)
 
     expect_equal(class(res), "numeric")
     expect_length(res, 8)

From 9a84af18a5e05448c5c8af84933b4fbdeea68edf Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 15:54:08 +0200
Subject: [PATCH 2/8] refactor: dataFrameFillDS, mergeDS, recodeValuesDS use
 .loadServersideObject

---
 R/dataFrameFillDS.R                       |  2 +-
 R/mergeDS.R                               | 15 ++---
 R/recodeValuesDS.R                        | 11 ++--
 tests/testthat/test-smk-dataFrameFillDS.R |  7 ++
 tests/testthat/test-smk-mergeDS.R         | 80 +++++++++++++++++++++++
 tests/testthat/test-smk-recodeValuesDS.R  | 16 +++++
 6 files changed, 112 insertions(+), 19 deletions(-)
 create mode 100644 tests/testthat/test-smk-mergeDS.R

diff --git a/R/dataFrameFillDS.R b/R/dataFrameFillDS.R
index 75f093f5..7f8d404a 100644
--- a/R/dataFrameFillDS.R
+++ b/R/dataFrameFillDS.R
@@ -21,7 +21,7 @@
 #' 
 dataFrameFillDS <- function(df.name, allNames.transmit, class.vect.transmit, levels.vec.transmit){
   
-  data <- eval(parse(text=df.name), envir = parent.frame())
+  data <- .loadServersideObject(df.name)
 
   if(!is.null(allNames.transmit)){
     allNames <- unlist(strsplit(allNames.transmit, split=","))
diff --git a/R/mergeDS.R b/R/mergeDS.R
index ce05ab7b..750cb3c9 100644
--- a/R/mergeDS.R
+++ b/R/mergeDS.R
@@ -78,19 +78,12 @@ mergeDS <- function(x.name, y.name, by.x.names.transmit, by.y.names.transmit, al
   }
   
 	# activate data frame names
-  x.data.frame <- eval(parse(text=x.name), envir = parent.frame())
-  y.data.frame <- eval(parse(text=y.name), envir = parent.frame())
+  x.data.frame <- .loadServersideObject(x.name)
+  y.data.frame <- .loadServersideObject(y.name)
 
   # check data.frames are valid data.frames
-  if(!is.data.frame(x.data.frame)){
-    studysideMessage <- "Error: x.name must specify a data.frame"
-    stop(studysideMessage, call. = FALSE)
-  }
-  
-  if(!is.data.frame(y.data.frame)){
-    studysideMessage <- "Error: y.name must specify a data.frame"
-    stop(studysideMessage, call. = FALSE)
-  }
+  .checkClass(obj = x.data.frame, obj_name = x.name, permitted_classes = c("data.frame"))
+  .checkClass(obj = y.data.frame, obj_name = y.name, permitted_classes = c("data.frame"))
 
   # manage by.x.names and by.y.names
 	# check text to be activated is not too long because of disclosure risk
diff --git a/R/recodeValuesDS.R b/R/recodeValuesDS.R
index d22a7862..73e57279 100644
--- a/R/recodeValuesDS.R
+++ b/R/recodeValuesDS.R
@@ -59,7 +59,7 @@ recodeValuesDS <- function(var.name.text=NULL, values2replace.text=NULL, new.val
     stop(studysideMessage, call. = FALSE)
   }
 
-  var2recode <- eval(parse(text=var.name.text), envir = parent.frame())
+  var2recode <- .loadServersideObject(var.name.text)
   
   values2replace <- unlist(strsplit(values2replace.text, split=","))
   new.values <- unlist(strsplit(new.values.text, split=","))
@@ -68,13 +68,10 @@ recodeValuesDS <- function(var.name.text=NULL, values2replace.text=NULL, new.val
   
   # get the class of the input variable
   var.class <- class(var2recode)
-  
-  # if the class of the input variable is not factor, numeric, character or integer then 
+
+  # if the class of the input variable is not factor, numeric, character or integer then
   # stop and return an error message
-  if (!(var.class %in% c('factor', 'character', 'numeric', 'integer'))){
-    studysideMessage <- "Error: The variable to recode must be either a factor, a character, a numeric or an integer"
-    stop(studysideMessage, call. = FALSE)
-  }
+  .checkClass(obj = var2recode, obj_name = var.name.text, permitted_classes = c('factor', 'character', 'numeric', 'integer'))
   
   # recode using the recode function from the dplyr package 
   if (var.class == 'factor'){
diff --git a/tests/testthat/test-smk-dataFrameFillDS.R b/tests/testthat/test-smk-dataFrameFillDS.R
index 8da7a882..326c6c85 100644
--- a/tests/testthat/test-smk-dataFrameFillDS.R
+++ b/tests/testthat/test-smk-dataFrameFillDS.R
@@ -90,6 +90,13 @@ test_that("simple dataFrameFillDS, ascending, numeric", {
     expect_equal(res.v6.levels[3], "3")
 })
 
+test_that("dataFrameFillDS errors when object does not exist", {
+    expect_error(
+        dataFrameFillDS("nonexistent_object", "a,b", "numeric,numeric", NULL),
+        regexp = "does not exist"
+    )
+})
+
 #
 # Shutdown
 #
diff --git a/tests/testthat/test-smk-mergeDS.R b/tests/testthat/test-smk-mergeDS.R
new file mode 100644
index 00000000..1fbac070
--- /dev/null
+++ b/tests/testthat/test-smk-mergeDS.R
@@ -0,0 +1,80 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+# context("mergeDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+test_that("mergeDS happy path, simple merge", {
+    x.df <- data.frame(id = c(1, 2, 3), val_x = c("a", "b", "c"))
+    y.df <- data.frame(id = c(1, 2, 3), val_y = c("d", "e", "f"))
+
+    res <- mergeDS("x.df", "y.df", "id", "id", FALSE, FALSE, TRUE, ".x,.y", TRUE, NULL)
+
+    expect_true(is.data.frame(res))
+    expect_true("val_x" %in% colnames(res))
+    expect_true("val_y" %in% colnames(res))
+    expect_equal(nrow(res), 3)
+})
+
+test_that("mergeDS errors when x.name object does not exist", {
+    y.df <- data.frame(id = c(1, 2, 3), val_y = c("d", "e", "f"))
+
+    expect_error(
+        mergeDS("nonexistent_object", "y.df", "id", "id", FALSE, FALSE, TRUE, ".x,.y", TRUE, NULL),
+        regexp = "does not exist"
+    )
+})
+
+test_that("mergeDS errors when y.name object does not exist", {
+    x.df <- data.frame(id = c(1, 2, 3), val_x = c("a", "b", "c"))
+
+    expect_error(
+        mergeDS("x.df", "nonexistent_object", "id", "id", FALSE, FALSE, TRUE, ".x,.y", TRUE, NULL),
+        regexp = "does not exist"
+    )
+})
+
+test_that("mergeDS errors when x.name is not a data.frame", {
+    x.df <- c(1, 2, 3)
+    y.df <- data.frame(id = c(1, 2, 3), val_y = c("d", "e", "f"))
+
+    expect_error(
+        mergeDS("x.df", "y.df", "id", "id", FALSE, FALSE, TRUE, ".x,.y", TRUE, NULL),
+        regexp = "must be of type"
+    )
+})
+
+test_that("mergeDS errors when y.name is not a data.frame", {
+    x.df <- data.frame(id = c(1, 2, 3), val_x = c("a", "b", "c"))
+    y.df <- c(1, 2, 3)
+
+    expect_error(
+        mergeDS("x.df", "y.df", "id", "id", FALSE, FALSE, TRUE, ".x,.y", TRUE, NULL),
+        regexp = "must be of type"
+    )
+})
+
+#
+# Done
+#
+
+# context("mergeDS::smk::shutdown")
+
+# context("mergeDS::smk::done")
diff --git a/tests/testthat/test-smk-recodeValuesDS.R b/tests/testthat/test-smk-recodeValuesDS.R
index 09b9e2f3..dcbe39b5 100644
--- a/tests/testthat/test-smk-recodeValuesDS.R
+++ b/tests/testthat/test-smk-recodeValuesDS.R
@@ -123,6 +123,22 @@ test_that("simple recodeValuesDS, character input with missings", {
   expect_true(is.na(res[7]))
 })
 
+test_that("recodeValuesDS errors when object does not exist", {
+    expect_error(
+        recodeValuesDS("nonexistent_object", "1,2", "10,20", NULL),
+        regexp = "does not exist"
+    )
+})
+
+test_that("recodeValuesDS errors when object has wrong type", {
+    input <- list(a = 1, b = 2)
+
+    expect_error(
+        recodeValuesDS("input", "1,2", "10,20", NULL),
+        regexp = "must be of type"
+    )
+})
+
 #
 # Done
 #

From 72253247c02be82f026f480a60fc44fc88b51ba5 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 15:54:22 +0200
Subject: [PATCH 3/8] refactor: cbindDS, dataFrameDS, rbindDS use
 .loadServersideObject

---
 R/cbindDS.R                           | 12 ++--
 R/dataFrameDS.R                       |  8 ++-
 R/rbindDS.R                           |  2 +-
 tests/testthat/test-smk-cbindDS.R     | 55 +++++++++++------
 tests/testthat/test-smk-dataFrameDS.R | 87 +++++++++++----------------
 tests/testthat/test-smk-rbindDS.R     | 62 +++++++++----------
 6 files changed, 115 insertions(+), 111 deletions(-)

diff --git a/R/cbindDS.R b/R/cbindDS.R
index b7864864..e0ad0b4c 100644
--- a/R/cbindDS.R
+++ b/R/cbindDS.R
@@ -28,11 +28,13 @@ cbindDS <- function(x.names.transmit=NULL, colnames.transmit=NULL){
   
   x.names.input <- x.names.transmit
   x.names.act1 <- unlist(strsplit(x.names.input, split=","))
-  x.names.act2 <- paste(x.names.act1, collapse=",")
-  
-  eval.code.x.names <- paste0("data.frame(", x.names.act2, ")")
-  
-  output.cbind <- eval(parse(text=eval.code.x.names), envir = parent.frame())
+
+  loaded.objects <- vector("list", length(x.names.act1))
+  for(i in seq_along(x.names.act1)) {
+    loaded.objects[[i]] <- .loadServersideObject(x.names.act1[i])
+  }
+
+  output.cbind <- do.call(data.frame, loaded.objects)
   
   colnames.input <- colnames.transmit
   colnames.act1 <- unlist(strsplit(colnames.input, split=","))
diff --git a/R/dataFrameDS.R b/R/dataFrameDS.R
index 7a2b36be..7f45c1af 100644
--- a/R/dataFrameDS.R
+++ b/R/dataFrameDS.R
@@ -58,8 +58,12 @@ dataFrameDS <- function(vectors=NULL, r.names=NULL, ch.rows=FALSE, ch.names=TRUE
     r.names <- unlist(r.names)
   }
   
-  eval.code.vectors.names <- paste0("data.frame(", vectors, ")")
-  dtemp0 <- eval(parse(text=eval.code.vectors.names), envir = parent.frame())
+  vectors.names <- unlist(strsplit(vectors, split=","))
+  loaded.vectors <- vector("list", length(vectors.names))
+  for(i in seq_along(vectors.names)) {
+    loaded.vectors[[i]] <- .loadServersideObject(vectors.names[i])
+  }
+  dtemp0 <- do.call(data.frame, loaded.vectors)
   
   dtemp <- data.frame(dtemp0, row.names=r.names, check.rows=ch.rows, check.names=ch.names,
                     stringsAsFactors=strAsFactors)
diff --git a/R/rbindDS.R b/R/rbindDS.R
index 71e88b17..5b0f6764 100644
--- a/R/rbindDS.R
+++ b/R/rbindDS.R
@@ -60,7 +60,7 @@ rbindDS<-function(x.names.transmit=NULL,colnames.transmit=NULL){
 
   rbind.matrix<-NULL
   for(k in numobj:1){
-    object.2.rbind<-eval(parse(text=x.names.active[k]), envir = parent.frame())
+    object.2.rbind<-.loadServersideObject(x.names.active[k])
 
     #coerce all input objects to data.matrix (like as.matrix but stays as numeric if numeric)
     object.2.rbind<-data.matrix(object.2.rbind)
diff --git a/tests/testthat/test-smk-cbindDS.R b/tests/testthat/test-smk-cbindDS.R
index 11fe1ef3..6a932cb3 100644
--- a/tests/testthat/test-smk-cbindDS.R
+++ b/tests/testthat/test-smk-cbindDS.R
@@ -15,36 +15,57 @@
 
 # context("cbindDS::smk::setup")
 
+set.standard.disclosure.settings()
+
 #
 # Tests
 #
 
-# context("cbindDS::smk::simple")
-test_that("simple cbindDS", {
-    inputs   <- 'input1,input2'
-    input1   <- c(0.0, 1.0, 2.0, 3.0)
-    input2   <- c(3.0, 2.0, 1.0, 0.0)
-    colnames <- 'v1,v2'
+test_that("cbindDS combines vectors into a data.frame", {
+    a <- c(1, 2, 3, 4, 5)
+    b <- c(10, 20, 30, 40, 50)
 
-    res <- cbindDS(inputs, colnames)
+    res <- cbindDS("a,b", "a,b")
 
     expect_equal(class(res), "data.frame")
-    expect_length(res, 2)
-    expect_equal(class(res[1]), "data.frame")
-    expect_equal(class(res[2]), "data.frame")
+    expect_equal(nrow(res), 5)
+    expect_equal(ncol(res), 2)
+    expect_equal(colnames(res), c("a", "b"))
+    expect_equal(res$a, a)
+    expect_equal(res$b, b)
+})
+
+test_that("cbindDS combines data.frame columns via $ syntax", {
+    df <- data.frame(x = c(1, 2, 3, 4, 5), y = c(6, 7, 8, 9, 10))
 
-    res.names <- names(res)
+    res <- cbindDS("df$x,df$y", "df$x,df$y")
 
-    expect_equal(class(res.names), "character")
-    expect_length(res.names, 2)
-    expect_equal(res.names[1], 'v1')
-    expect_equal(res.names[2], 'v2')
+    expect_equal(class(res), "data.frame")
+    expect_equal(nrow(res), 5)
+    expect_equal(ncol(res), 2)
+    expect_equal(colnames(res), c("x", "y"))
+    expect_equal(res$x, df$x)
+    expect_equal(res$y, df$y)
+})
+
+test_that("cbindDS makes duplicate column names unique", {
+    a <- c(1, 2, 3, 4, 5)
+    b <- c(10, 20, 30, 40, 50)
+
+    res <- cbindDS("a,b", "v,v")
+
+    expect_equal(colnames(res), c("v", "v.1"))
+})
+
+test_that("cbindDS errors when object does not exist", {
+    expect_error(
+        cbindDS("nonexistent_obj", "nonexistent_obj"),
+        regexp = "does not exist"
+    )
 })
 
 #
 # Done
 #
 
-# context("cbindDS::smk::shutdown")
-
 # context("cbindDS::smk::done")
diff --git a/tests/testthat/test-smk-dataFrameDS.R b/tests/testthat/test-smk-dataFrameDS.R
index 18fc3b4b..441e5ef9 100644
--- a/tests/testthat/test-smk-dataFrameDS.R
+++ b/tests/testthat/test-smk-dataFrameDS.R
@@ -21,68 +21,51 @@ set.standard.disclosure.settings()
 # Tests
 #
 
-# context("dataFrameDS::smk")
-test_that("simple dataFrameDS", {
-    v1            <- c(0.0, 1.0, 2.0, 3.0, 4.0)
-    v2            <- c(4.0, 3.0, 2.0, 1.0, 0.0)
-    vectors       <- "v1,v2"
-    r.names       <- NULL
-    ch.rows       <- FALSE
-    ch.names      <- FALSE
-    clnames       <- "x1,x2"
-    strAsFactors  <- FALSE
-    completeCases <- FALSE
-
-    res <- dataFrameDS(vectors, r.names, ch.rows, ch.names, clnames, strAsFactors, completeCases)
+test_that("dataFrameDS creates a data.frame from vectors", {
+    a <- c(1, 2, 3, 4, 5)
+    b <- c(10, 20, 30, 40, 50)
+
+    res <- dataFrameDS("a,b", r.names=NULL, ch.rows=FALSE, ch.names=TRUE,
+                       clnames="a,b", strAsFactors=TRUE, completeCases=FALSE)
 
     expect_equal(class(res), "data.frame")
-    expect_length(res, 2)
-
-    res.classes <- colnames(res)
-    expect_length(res.classes, 2)
-    expect_equal(res.classes[1], "x1")
-    expect_equal(res.classes[2], "x2")
-
-    for (index in 1:length(res))
-    {
-        expect_equal(v1[index], res$x1[index], info = paste0('index=', index, ', column=x1'))
-        expect_equal(v2[index], res$x2[index], info = paste0('index=', index, ', column=x2'))
-    }
+    expect_equal(nrow(res), 5)
+    expect_equal(ncol(res), 2)
+    expect_equal(colnames(res), c("a", "b"))
+    expect_equal(res$a, a)
+    expect_equal(res$b, b)
 })
 
-test_that("simple dataFrameDS, strAsFactors is TRUE", {
-    v1            <- c(0.0, 1.0, 2.0, 3.0, 4.0)
-    v2            <- c(4.0, 3.0, 2.0, 1.0, 0.0)
-    vectors       <- "v1,v2"
-    r.names       <- NULL
-    ch.rows       <- FALSE
-    ch.names      <- FALSE
-    clnames       <- "x1,x2"
-    strAsFactors  <- TRUE
-    completeCases <- FALSE
+test_that("dataFrameDS handles $ column name syntax", {
+    df <- data.frame(x = c(1, 2, 3, 4, 5), y = c(6, 7, 8, 9, 10))
 
-    res <- dataFrameDS(vectors, r.names, ch.rows, ch.names, clnames, strAsFactors, completeCases)
+    res <- dataFrameDS("df$x,df$y", r.names=NULL, ch.rows=FALSE, ch.names=TRUE,
+                       clnames="df$x,df$y", strAsFactors=TRUE, completeCases=FALSE)
 
     expect_equal(class(res), "data.frame")
-    expect_length(res, 2)
-
-    res.classes <- colnames(res)
-    expect_length(res.classes, 2)
-    expect_equal(res.classes[1], "x1")
-    expect_equal(res.classes[2], "x2")
-
-    for (index in 1:length(res))
-    {
-        expect_equal(v1[index], res$x1[index], info = paste0('index=', index, ', column=x1'))
-        expect_equal(v2[index], res$x2[index], info = paste0('index=', index, ', column=x2'))
-    }
+    expect_equal(colnames(res), c("x", "y"))
+    expect_equal(res$x, df$x)
+    expect_equal(res$y, df$y)
 })
 
-#
-# Stutdown
-#
+test_that("dataFrameDS removes rows with NAs when completeCases is TRUE", {
+    a <- c(1, NA, 3, 4, 5)
+    b <- c(10, 20, NA, 40, 50)
+
+    res <- dataFrameDS("a,b", r.names=NULL, ch.rows=FALSE, ch.names=TRUE,
+                       clnames="a,b", strAsFactors=TRUE, completeCases=TRUE)
 
-# context("dataFrameDS::smk::shutdown")
+    expect_equal(class(res), "data.frame")
+    expect_equal(nrow(res), 3)
+})
+
+test_that("dataFrameDS errors when object does not exist", {
+    expect_error(
+        dataFrameDS("nonexistent_obj", r.names=NULL, ch.rows=FALSE, ch.names=TRUE,
+                     clnames="nonexistent_obj", strAsFactors=TRUE, completeCases=FALSE),
+        regexp = "does not exist"
+    )
+})
 
 #
 # Done
diff --git a/tests/testthat/test-smk-rbindDS.R b/tests/testthat/test-smk-rbindDS.R
index 7f757a1e..af99483b 100644
--- a/tests/testthat/test-smk-rbindDS.R
+++ b/tests/testthat/test-smk-rbindDS.R
@@ -15,53 +15,47 @@
 
 # context("rbindDS::smk::setup")
 
+set.standard.disclosure.settings()
+
 #
 # Tests
 #
 
-# context("rbindDS::smk::simple")
-test_that("simple rbindDS", {
-    inputs   <- 'input1, input2'
-    input1   <- c(0.0, 1.0, 2.0, 3.0)
-    input2   <- c(3.0, 2.0, 1.0, 0.0)
-    colnames <- 'v1'
+test_that("rbindDS combines two data.frames by row", {
+    df1 <- data.frame(a = c(1, 2, 3), b = c(4, 5, 6))
+    df2 <- data.frame(a = c(7, 8), b = c(9, 10))
 
-    res <- rbindDS(inputs, colnames)
+    res <- rbindDS("df1,df2", "a,b")
 
-    res.class <- class(res)
-    if (base::getRversion() < '4.0.0')
-    {
-        expect_length(res.class, 1)
-        expect_true("matrix" %in% res.class)
-    }
-    else
-    {
-        expect_length(res.class, 2)
-        expect_true("matrix" %in% res.class)
-        expect_true("array" %in% res.class)
-    }
+    expect_true(is.matrix(res))
+    expect_equal(nrow(res), 5)
+    expect_equal(ncol(res), 2)
+    expect_equal(colnames(res), c("a", "b"))
+    expect_equal(res[, "a"], c(1, 2, 3, 7, 8))
+    expect_equal(res[, "b"], c(4, 5, 6, 9, 10))
+})
 
-    expect_length(res, 8)
-    expect_equal(class(res[1]), "numeric")
-    expect_equal(class(res[2]), "numeric")
-    expect_equal(class(res[3]), "numeric")
-    expect_equal(class(res[4]), "numeric")
-    expect_equal(class(res[5]), "numeric")
-    expect_equal(class(res[6]), "numeric")
-    expect_equal(class(res[7]), "numeric")
-    expect_equal(class(res[8]), "numeric")
+test_that("rbindDS combines vectors", {
+    v1 <- c(1, 2, 3)
+    v2 <- c(4, 5, 6)
 
-    res.colnames <- colnames(res)
+    res <- rbindDS("v1,v2", "V1")
 
-    expect_equal(class(res.colnames), "character")
-    expect_length(res.colnames, 1)
-    expect_equal(res.colnames[1], 'v1')
+    expect_true(is.matrix(res))
+    expect_equal(nrow(res), 6)
+    expect_equal(ncol(res), 1)
+    expect_equal(colnames(res), "V1")
+})
+
+test_that("rbindDS errors when object does not exist", {
+    expect_error(
+        rbindDS("nonexistent_obj", "a"),
+        regexp = "does not exist"
+    )
 })
 
 #
 # Done
 #
 
-# context("rbindDS::smk::shutdown")
-
 # context("rbindDS::smk::done")

From 2554c55473ed0b6c65772d31cbf1f7fb72d1f597 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 13 Apr 2026 15:54:32 +0200
Subject: [PATCH 4/8] refactor: complex functions use .loadServersideObject

---
 R/BooleDS.R                                  |  4 +-
 R/dataFrameSortDS.R                          |  5 +-
 R/dataFrameSubsetDS1.R                       | 15 +++-
 R/dataFrameSubsetDS2.R                       | 15 +++-
 R/repDS.R                                    |  8 +-
 R/seqDS.R                                    | 22 +++---
 tests/testthat/test-smk-BooleDS.R            | 20 +++++
 tests/testthat/test-smk-dataFrameSortDS.R    | 16 ++++
 tests/testthat/test-smk-dataFrameSubsetDS1.R | 22 ++++++
 tests/testthat/test-smk-dataFrameSubsetDS2.R | 22 ++++++
 tests/testthat/test-smk-repDS.R              | 83 ++++++++++++++++++++
 tests/testthat/test-smk-seqDS.R              | 17 ++++
 12 files changed, 223 insertions(+), 26 deletions(-)
 create mode 100644 tests/testthat/test-smk-repDS.R

diff --git a/R/BooleDS.R b/R/BooleDS.R
index 0f54dfca..70c81941 100644
--- a/R/BooleDS.R
+++ b/R/BooleDS.R
@@ -50,8 +50,8 @@ thr <- dsBase::listDisclosureSettingsDS()                               #
 
 ##########CHECK NOT LONG SPECIFIED VECTOR##############
 
-V1<-eval(parse(text=V1.name), envir = parent.frame())
-V2<-eval(parse(text=V2.name), envir = parent.frame())
+V1<-.loadServersideObject(V1.name)
+V2<-.loadServersideObject(V2.name)
 
 
 if(is.character(V1)){
diff --git a/R/dataFrameSortDS.R b/R/dataFrameSortDS.R
index a398a70b..ec7f5e97 100644
--- a/R/dataFrameSortDS.R
+++ b/R/dataFrameSortDS.R
@@ -65,9 +65,8 @@ dataFrameSortDS <- function(df.name=NULL,sort.key.name=NULL,sort.descending,sort
     stop(studysideMessage, call. = FALSE)
   }
 
-  df.name.2 <- paste0("data.frame(",df.name,")")
-  df2sort   <- eval(parse(text=df.name.2), envir = parent.frame())
-  sort.key  <- eval(parse(text=sort.key.name), envir = parent.frame())
+  df2sort   <- data.frame(.loadServersideObject(df.name))
+  sort.key  <- .loadServersideObject(sort.key.name)
 
   # TYPE CHECK
   if(any(class(sort.key) %in% 'factor')){
diff --git a/R/dataFrameSubsetDS1.R b/R/dataFrameSubsetDS1.R
index 4b3c9476..1c76c1ca 100644
--- a/R/dataFrameSubsetDS1.R
+++ b/R/dataFrameSubsetDS1.R
@@ -157,8 +157,7 @@ if(sum(is.na(keep.code.n))>0){
     }
   }
 
-  df.name.2 <- paste0("data.frame(",df.name,")")
-  df2subset <- eval(parse(text=df.name.2), envir = parent.frame())
+  df2subset <- data.frame(.loadServersideObject(df.name))
 
   if(V1.name=="ONES"||V2.name=="ONES")
   {
@@ -175,8 +174,16 @@ if(sum(is.na(keep.code.n))>0){
       ONES<-V1
     }
   } else {
-     V1 <- eval(parse(text=V1.name), envir = parent.frame())
-     V2 <- eval(parse(text=V2.name), envir = parent.frame())
+     V1 <- tryCatch(.loadServersideObject(V1.name), error = function(e) {
+       numeric.val <- suppressWarnings(as.numeric(V1.name))
+       if (is.na(numeric.val)) stop(e)
+       numeric.val
+     })
+     V2 <- tryCatch(.loadServersideObject(V2.name), error = function(e) {
+       numeric.val <- suppressWarnings(as.numeric(V2.name))
+       if (is.na(numeric.val)) stop(e)
+       numeric.val
+     })
   }
 
   ##########CHECK APPROPRIATE CLASSES ##############
diff --git a/R/dataFrameSubsetDS2.R b/R/dataFrameSubsetDS2.R
index 05938a60..8a9a6ed6 100644
--- a/R/dataFrameSubsetDS2.R
+++ b/R/dataFrameSubsetDS2.R
@@ -177,8 +177,7 @@ if(!is.null(V2.name)){
 }
 
 
-   df.name.2<-paste0("data.frame(",df.name,")")
-   df2subset <- eval(parse(text=df.name.2), envir = parent.frame())
+   df2subset <- data.frame(.loadServersideObject(df.name))
 
    if(V1.name=="ONES"||V2.name=="ONES")
    {
@@ -195,8 +194,16 @@ if(!is.null(V2.name)){
        ONES<-V1
      }
    }else{
-     V1<-eval(parse(text=V1.name), envir = parent.frame())
-     V2<-eval(parse(text=V2.name), envir = parent.frame())
+     V1<-tryCatch(.loadServersideObject(V1.name), error = function(e) {
+       numeric.val <- suppressWarnings(as.numeric(V1.name))
+       if (is.na(numeric.val)) stop(e)
+       numeric.val
+     })
+     V2<-tryCatch(.loadServersideObject(V2.name), error = function(e) {
+       numeric.val <- suppressWarnings(as.numeric(V2.name))
+       if (is.na(numeric.val)) stop(e)
+       numeric.val
+     })
    }
 
 
diff --git a/R/repDS.R b/R/repDS.R
index 61b4e3ea..f6454ea2 100644
--- a/R/repDS.R
+++ b/R/repDS.R
@@ -175,7 +175,7 @@ if(source.x1=="serverside")
 {
 #x1.transmit is the name of a serverside vector or scalar
 
-x1.use<-eval(parse(text=x1.transmit), envir = parent.frame())
+x1.use<-.loadServersideObject(x1.transmit)
 }
 
 if(source.x1=="clientside")
@@ -276,7 +276,7 @@ else
 	{
 	#times.transmit is the name of a serverside vector or scalar
 
-	times.use<-eval(parse(text=times.transmit), envir = parent.frame())
+	times.use<-.loadServersideObject(times.transmit)
 	}
 
 	if(source.times=="clientside")
@@ -364,7 +364,7 @@ else
 	if(source.length.out=="serverside")
 	{
 	#length.out.transmit is the name of the serverside vector or scalar
-	length.out.temp<-eval(parse(text=length.out.transmit), envir = parent.frame())
+	length.out.temp<-.loadServersideObject(length.out.transmit)
 	
 	arg.is.vector<-FALSE
 	if(length(length.out.temp)>=2)arg.is.vector<-TRUE
@@ -460,7 +460,7 @@ else
 	if(source.each=="serverside")
 	{
 	#each.transmit is the name of the serverside vector or scalar
-	each.use<-eval(parse(text=each.transmit), envir = parent.frame())
+	each.use<-.loadServersideObject(each.transmit)
 	}
 
 	if(source.each=="clientside")
diff --git a/R/seqDS.R b/R/seqDS.R
index 97df7c3e..e8af69aa 100644
--- a/R/seqDS.R
+++ b/R/seqDS.R
@@ -65,8 +65,9 @@ nfilter.subset<-as.numeric(thr$nfilter.subset)                          #
 #########################################################################
 
 
- if(is.character(FROM.value.char)&&is.numeric(eval(parse(text=FROM.value.char), envir = parent.frame()))){
-	FROM<-eval(parse(text=FROM.value.char), envir = parent.frame())
+ FROM.eval <- tryCatch(.loadServersideObject(FROM.value.char), error = function(e) as.numeric(FROM.value.char))
+ if(is.character(FROM.value.char)&&is.numeric(FROM.eval)){
+	FROM<-FROM.eval
 	}else{
    studysideMessage<-"ERROR: FROM.value.char must be specified as a real number in inverted commas eg '-3.74' or '0'"
    stop(studysideMessage, call. = FALSE)
@@ -74,9 +75,10 @@ nfilter.subset<-as.numeric(thr$nfilter.subset)                          #
  
  if(!is.null(TO.value.char))
 	{
-	if(is.character(TO.value.char)&&is.numeric(eval(parse(text=TO.value.char), envir = parent.frame())))
+	TO.eval <- tryCatch(.loadServersideObject(TO.value.char), error = function(e) as.numeric(TO.value.char))
+	if(is.character(TO.value.char)&&is.numeric(TO.eval))
 		{
-		TO<-eval(parse(text=TO.value.char), envir = parent.frame())
+		TO<-TO.eval
 		}else{
 		studysideMessage<-"ERROR: TO.value.char must be specified as a real number in inverted commas eg '-3.74' or '0'"
 		stop(studysideMessage, call. = FALSE)
@@ -88,16 +90,18 @@ nfilter.subset<-as.numeric(thr$nfilter.subset)                          #
  TO<-NULL
  }
 	
- if(is.character(BY.value.char)&&is.numeric(eval(parse(text=BY.value.char), envir = parent.frame()))){
-	BY<-eval(parse(text=BY.value.char), envir = parent.frame())
+ BY.eval <- tryCatch(.loadServersideObject(BY.value.char), error = function(e) as.numeric(BY.value.char))
+ if(is.character(BY.value.char)&&is.numeric(BY.eval)){
+	BY<-BY.eval
 	}else{
    studysideMessage<-"ERROR: BY.value.char must be specified as a real number in inverted commas eg '-3.74' or '0'"
    stop(studysideMessage, call. = FALSE)
    }
 
  if(!is.null(LENGTH.OUT.value.char)){
-		if(is.character(LENGTH.OUT.value.char)&&is.numeric(eval(parse(text=LENGTH.OUT.value.char), envir = parent.frame()))){
-		LENGTH.OUT<-eval(parse(text=LENGTH.OUT.value.char), envir = parent.frame())
+		LENGTH.OUT.eval <- tryCatch(.loadServersideObject(LENGTH.OUT.value.char), error = function(e) as.numeric(LENGTH.OUT.value.char))
+		if(is.character(LENGTH.OUT.value.char)&&is.numeric(LENGTH.OUT.eval)){
+		LENGTH.OUT<-LENGTH.OUT.eval
 		}else{
 		studysideMessage<-"ERROR: If LENGTH.OUT.value.char is non-NULL, it must specify a positive integer in inverted commas eg '14'" 
 		stop(studysideMessage, call. = FALSE)
@@ -110,7 +114,7 @@ nfilter.subset<-as.numeric(thr$nfilter.subset)                          #
  
  if(!is.null(ALONG.WITH.name)){
 		if(is.character(ALONG.WITH.name)){
-		ALONG.WITH<-eval(parse(text=ALONG.WITH.name), envir = parent.frame())
+		ALONG.WITH<-.loadServersideObject(ALONG.WITH.name)
 		}else{
 		studysideMessage<-"ERROR: If ALONG.WITH.name is non-NULL, it must specify the name of a serverside vector in inverted commas" 
 		stop(studysideMessage, call. = FALSE)
diff --git a/tests/testthat/test-smk-BooleDS.R b/tests/testthat/test-smk-BooleDS.R
index 5fcfa4ee..685dc0fa 100644
--- a/tests/testthat/test-smk-BooleDS.R
+++ b/tests/testthat/test-smk-BooleDS.R
@@ -15,6 +15,8 @@
 
 # context("BooleDS::smk::setup")
 
+set.standard.disclosure.settings()
+
 #
 # Tests
 #
@@ -279,6 +281,24 @@ test_that("na-check BooleDS, logical, NA=1", {
     expect_equal(res[5], TRUE)
 })
 
+test_that("BooleDS errors when V1 object does not exist", {
+    input <- data.frame(v2 = c(1.0, 2.0, 3.0, 4.0, 5.0))
+
+    expect_error(
+        BooleDS("nonexistent$v1", "input$v2", 1, "NA", TRUE),
+        regexp = "does not exist"
+    )
+})
+
+test_that("BooleDS errors when V2 object does not exist", {
+    input <- data.frame(v1 = c(1.0, 2.0, 3.0, 4.0, 5.0))
+
+    expect_error(
+        BooleDS("input$v1", "nonexistent$v2", 1, "NA", TRUE),
+        regexp = "does not exist"
+    )
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-dataFrameSortDS.R b/tests/testthat/test-smk-dataFrameSortDS.R
index 39a7378b..a61a4c62 100644
--- a/tests/testthat/test-smk-dataFrameSortDS.R
+++ b/tests/testthat/test-smk-dataFrameSortDS.R
@@ -468,6 +468,22 @@ test_that("simple dataFrameSortDS, descending, alphabetic", {
     expect_equal(res$v2[8], "6.0")
 })
 
+test_that("dataFrameSortDS errors when df does not exist", {
+    expect_error(
+        dataFrameSortDS("nonexistent", "nonexistent$v1", FALSE, "default"),
+        regexp = "does not exist"
+    )
+})
+
+test_that("dataFrameSortDS errors when sort key does not exist", {
+    df <- data.frame(v1 = c(1, 2, 3, 4, 5, 6, 7, 8), v2 = c(1, 2, 3, 4, 5, 6, 7, 8))
+
+    expect_error(
+        dataFrameSortDS("df", "nonexistent$col", FALSE, "default"),
+        regexp = "does not exist"
+    )
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-dataFrameSubsetDS1.R b/tests/testthat/test-smk-dataFrameSubsetDS1.R
index c519cefa..b70c7993 100644
--- a/tests/testthat/test-smk-dataFrameSubsetDS1.R
+++ b/tests/testthat/test-smk-dataFrameSubsetDS1.R
@@ -74,6 +74,28 @@ test_that("test2 dataFrameSubsetDS1", {
   
 })
 
+test_that("dataFrameSubsetDS1 errors when df does not exist", {
+    expect_error(
+        dataFrameSubsetDS1(df.name="nonexistent", V1.name="x", V2.name="1",
+                           Boolean.operator.n=1, keep.NAs=FALSE),
+        regexp = "does not exist"
+    )
+})
+
+test_that("dataFrameSubsetDS1 errors when V1 object does not exist", {
+    D <- as.data.frame(matrix(NA, nrow=20, ncol=3))
+    colnames(D) <- c('integer','numeric','binary')
+    D$integer <- rep(1, 20)
+    D$numeric <- rep(1, 20)
+    D$binary <- rep(1, 20)
+
+    expect_error(
+        dataFrameSubsetDS1(df.name="D", V1.name="nonexistent$col", V2.name="1",
+                           Boolean.operator.n=1, keep.NAs=FALSE),
+        regexp = "does not exist"
+    )
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-dataFrameSubsetDS2.R b/tests/testthat/test-smk-dataFrameSubsetDS2.R
index c93dc595..99968ee4 100644
--- a/tests/testthat/test-smk-dataFrameSubsetDS2.R
+++ b/tests/testthat/test-smk-dataFrameSubsetDS2.R
@@ -71,6 +71,28 @@ test_that("test2 dataFrameSubsetDS2", {
   
 })
 
+test_that("dataFrameSubsetDS2 errors when df does not exist", {
+    expect_error(
+        dataFrameSubsetDS2(df.name="nonexistent", V1.name="x", V2.name="1",
+                           Boolean.operator.n=1, keep.NAs=FALSE),
+        regexp = "does not exist"
+    )
+})
+
+test_that("dataFrameSubsetDS2 errors when V1 object does not exist", {
+    D <- as.data.frame(matrix(NA, nrow=20, ncol=3))
+    colnames(D) <- c('integer','numeric','binary')
+    D$integer <- rep(1, 20)
+    D$numeric <- rep(1, 20)
+    D$binary <- rep(1, 20)
+
+    expect_error(
+        dataFrameSubsetDS2(df.name="D", V1.name="nonexistent$col", V2.name="1",
+                           Boolean.operator.n=1, keep.NAs=FALSE),
+        regexp = "does not exist"
+    )
+})
+
 #
 # Done
 #
diff --git a/tests/testthat/test-smk-repDS.R b/tests/testthat/test-smk-repDS.R
new file mode 100644
index 00000000..c4929f47
--- /dev/null
+++ b/tests/testthat/test-smk-repDS.R
@@ -0,0 +1,83 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+# context("repDS::smk::setup")
+
+set.standard.disclosure.settings()
+
+#
+# Tests
+#
+
+test_that("repDS with serverside scalar x1", {
+    myScalar <- 5
+
+    res <- repDS(x1.transmit="myScalar", times.transmit="3", length.out.transmit=NULL,
+                 each.transmit=NULL, x1.includes.characters=FALSE,
+                 source.x1="serverside", source.times="clientside",
+                 source.length.out=NULL, source.each=NULL)
+
+    expect_equal(res, c(5, 5, 5))
+})
+
+test_that("repDS with serverside vector x1", {
+    myVec <- c(1, 2, 3)
+
+    res <- repDS(x1.transmit="myVec", times.transmit="2", length.out.transmit=NULL,
+                 each.transmit=NULL, x1.includes.characters=FALSE,
+                 source.x1="serverside", source.times="clientside",
+                 source.length.out=NULL, source.each=NULL)
+
+    expect_equal(res, c(1, 2, 3, 1, 2, 3))
+})
+
+test_that("repDS with clientside x1", {
+    res <- repDS(x1.transmit="7", times.transmit="4", length.out.transmit=NULL,
+                 each.transmit=NULL, x1.includes.characters=FALSE,
+                 source.x1="clientside", source.times="clientside",
+                 source.length.out=NULL, source.each=NULL)
+
+    expect_equal(res, c(7, 7, 7, 7))
+})
+
+test_that("repDS errors when serverside x1 object does not exist", {
+    expect_error(
+        repDS(x1.transmit="nonexistent_obj", times.transmit="3", length.out.transmit=NULL,
+              each.transmit=NULL, x1.includes.characters=FALSE,
+              source.x1="serverside", source.times="clientside",
+              source.length.out=NULL, source.each=NULL),
+        regexp = "does not exist"
+    )
+})
+
+test_that("repDS errors when serverside times object does not exist", {
+    myScalar <- 5
+
+    expect_error(
+        repDS(x1.transmit="myScalar", times.transmit="nonexistent_times", length.out.transmit=NULL,
+              each.transmit=NULL, x1.includes.characters=FALSE,
+              source.x1="serverside", source.times="serverside",
+              source.length.out=NULL, source.each=NULL),
+        regexp = "does not exist"
+    )
+})
+
+#
+# Done
+#
+
+# context("repDS::smk::shutdown")
+
+# context("repDS::smk::done")
diff --git a/tests/testthat/test-smk-seqDS.R b/tests/testthat/test-smk-seqDS.R
index 7cdd62eb..3a9edfb6 100644
--- a/tests/testthat/test-smk-seqDS.R
+++ b/tests/testthat/test-smk-seqDS.R
@@ -118,6 +118,23 @@ test_that("simple seqDS", {
     expect_equal(res[7], 1.5)
 })
 
+test_that("seqDS with ALONG.WITH server-side vector", {
+    myVec <- c(10, 20, 30, 40, 50)
+
+    res <- seqDS("1", NULL, "1", NULL, "myVec")
+
+    expect_equal(class(res), "numeric")
+    expect_length(res, 5)
+    expect_equal(res, c(1, 2, 3, 4, 5))
+})
+
+test_that("seqDS errors when ALONG.WITH object does not exist", {
+    expect_error(
+        seqDS("1", NULL, "1", NULL, "nonexistent_obj"),
+        regexp = "does not exist"
+    )
+})
+
 #
 # Done
 #

From 103057969af3fef80fa81daa6b849d79983ac72a Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 14 Apr 2026 23:36:20 +0200
Subject: [PATCH 5/8] refactor: cDS and listDS use .loadServersideObject

---
 R/cDS.R                          | 24 +++++++++++++-----------
 R/listDS.R                       | 17 ++++++++++-------
 tests/testthat/test-smk-cDS.R    | 16 +++++++---------
 tests/testthat/test-smk-listDS.R |  5 +++--
 4 files changed, 33 insertions(+), 29 deletions(-)

diff --git a/R/cDS.R b/R/cDS.R
index 0b5b96ba..c326cf85 100644
--- a/R/cDS.R
+++ b/R/cDS.R
@@ -3,28 +3,30 @@
 #' @description This function is similar to the R base function 'c'.
 #' @details Unlike the R base function 'c' on vector or list of certain 
 #' length are allowed as output
-#' @param objs a list which contains the the objects to concatenate.
+#' @param x.names a character vector of object names to concatenate.
 #' @return a vector or list
 #' @author Gaye, A.
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#' 
-cDS <- function (objs) {
-  
+#'
+cDS <- function (x.names) {
+
   # Check Permissive Privacy Control Level.
   dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'avocado'))
-  
-  # this filter sets the minimum number of observations that are allowed 
+
+  # this filter sets the minimum number of observations that are allowed
 
   #############################################################
   # MODULE 1: CAPTURE THE nfilter SETTINGS
   thr <- dsBase::listDisclosureSettingsDS()
   nfilter.tab <- as.numeric(thr$nfilter.tab)
-  #nfilter.glm <- as.numeric(thr$nfilter.glm)
-  #nfilter.subset <- as.numeric(thr$nfilter.subset)
-  #nfilter.string <- as.numeric(thr$nfilter.string)
   #############################################################
-  
-  x <-  unlist(objs)
+
+  objs <- list()
+  for (i in seq_along(x.names)) {
+    objs[[i]] <- .loadServersideObject(x.names[i])
+  }
+  x <- unlist(objs)
 
   # check if the output is valid and output accordingly
   if(length(x) < nfilter.tab){
diff --git a/R/listDS.R b/R/listDS.R
index 162ae8b5..a08df9b8 100644
--- a/R/listDS.R
+++ b/R/listDS.R
@@ -3,17 +3,20 @@
 #' @description this function is similar to R function 'list'
 #' @details Unlike the R function 'list' it takes also a vector of characters,
 #' the names of the elements in the output list.
-#' @param input a list of objects to coerce into a list
-#' @param eltnames a character list, the names of the elements in the list.
+#' @param x.names a character vector of object names to coerce into a list.
+#' @param eltnames a character vector, the names of the elements in the list.
 #' @return a list
 #' @author Gaye, A.
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
-#' 
-listDS <-function (input=NULL, eltnames=NULL){
-  
-  mylist <- input
+#'
+listDS <- function (x.names = NULL, eltnames = NULL) {
+
+  mylist <- list()
+  for (i in seq_along(x.names)) {
+    mylist[[i]] <- .loadServersideObject(x.names[i])
+  }
   names(mylist) <- unlist(eltnames)
 
   return(mylist)
-  
 }
\ No newline at end of file
diff --git a/tests/testthat/test-smk-cDS.R b/tests/testthat/test-smk-cDS.R
index 0f9842fc..518d9ac5 100644
--- a/tests/testthat/test-smk-cDS.R
+++ b/tests/testthat/test-smk-cDS.R
@@ -23,9 +23,9 @@ set.standard.disclosure.settings()
 
 # context("cDS::smk::numeric list")
 test_that("numeric list cDS", {
-    input <- list(a=0.0, b=1.0, c=2.0, d=3.0)
+    a <- 0.0; b <- 1.0; c <- 2.0; d <- 3.0
 
-    res <- cDS(input)
+    res <- cDS(c("a", "b", "c", "d"))
 
     expect_length(res, 4)
     expect_equal(class(res), "numeric")
@@ -37,9 +37,9 @@ test_that("numeric list cDS", {
 
 # context("cDS::smk::character list")
 test_that("character list cDS", {
-    input <- list(a="0.0", b="1.0", c="2.0", d="3.0")
+    a <- "0.0"; b <- "1.0"; c <- "2.0"; d <- "3.0"
 
-    res <- cDS(input)
+    res <- cDS(c("a", "b", "c", "d"))
 
     expect_length(res, 4)
     expect_equal(class(res), "character")
@@ -51,9 +51,9 @@ test_that("character list cDS", {
 
 # context("cDS::smk::numeric list small")
 test_that("single numeric list small cDS", {
-    input <- list(a=0, b=1)
+    a <- 0; b <- 1
 
-    res <- cDS(input)
+    res <- cDS(c("a", "b"))
 
     expect_length(res, 2)
     expect_equal(class(res), "logical")
@@ -63,9 +63,7 @@ test_that("single numeric list small cDS", {
 
 # context("cDS::smk::empty list")
 test_that("empty list cDS", {
-    input <- list()
-
-    res <- cDS(input)
+    res <- cDS(character(0))
 
     expect_length(res, 0)
     expect_equal(class(res), "NULL")
diff --git a/tests/testthat/test-smk-listDS.R b/tests/testthat/test-smk-listDS.R
index dfd0a171..51e75550 100644
--- a/tests/testthat/test-smk-listDS.R
+++ b/tests/testthat/test-smk-listDS.R
@@ -21,10 +21,11 @@
 
 # context("listDS::smk::simple")
 test_that("simple listDS", {
-    input    <- list(v1 = c(1, 2, 3), v2 = c(4, 5, 6))
+    v1 <- c(1, 2, 3)
+    v2 <- c(4, 5, 6)
     eltnames <- c('n1', 'n2')
 
-    res <- listDS(input, eltnames)
+    res <- listDS(c("v1", "v2"), eltnames)
 
     expect_equal(class(res), "list")
     expect_length(res, 2)

From ab54ce0f5e0a09b7a3df36df90e9be4d54d00a40 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 14 Apr 2026 23:36:20 +0200
Subject: [PATCH 6/8] fix: BooleDS accepts literal scalar V2

---
 R/BooleDS.R | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/BooleDS.R b/R/BooleDS.R
index 70c81941..b7e48490 100644
--- a/R/BooleDS.R
+++ b/R/BooleDS.R
@@ -51,7 +51,14 @@ thr <- dsBase::listDisclosureSettingsDS()                               #
 ##########CHECK NOT LONG SPECIFIED VECTOR##############
 
 V1<-.loadServersideObject(V1.name)
-V2<-.loadServersideObject(V2.name)
+
+# V2 may be either a server-side object name or a literal scalar (e.g. "3", "-1")
+V2.numeric <- suppressWarnings(as.numeric(V2.name))
+if(!is.na(V2.numeric)){
+  V2 <- V2.numeric
+}else{
+  V2 <- .loadServersideObject(V2.name)
+}
 
 
 if(is.character(V1)){

From e5b300c593bda98388c2d74ffe75b75bc6270561 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 14 Apr 2026 23:44:07 +0200
Subject: [PATCH 7/8] docs: redocument batch-4

---
 man/cDS.Rd         | 6 ++++--
 man/listDS.Rd      | 8 +++++---
 man/replaceNaDS.Rd | 4 ++--
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/man/cDS.Rd b/man/cDS.Rd
index 7b4e448a..e3da7bf2 100644
--- a/man/cDS.Rd
+++ b/man/cDS.Rd
@@ -4,10 +4,10 @@
 \alias{cDS}
 \title{Concatenates objects into a vector or list}
 \usage{
-cDS(objs)
+cDS(x.names)
 }
 \arguments{
-\item{objs}{a list which contains the the objects to concatenate.}
+\item{x.names}{a character vector of object names to concatenate.}
 }
 \value{
 a vector or list
@@ -21,4 +21,6 @@ length are allowed as output
 }
 \author{
 Gaye, A.
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/listDS.Rd b/man/listDS.Rd
index 36b1c236..4f0401a1 100644
--- a/man/listDS.Rd
+++ b/man/listDS.Rd
@@ -4,12 +4,12 @@
 \alias{listDS}
 \title{Coerce objects into a list}
 \usage{
-listDS(input = NULL, eltnames = NULL)
+listDS(x.names = NULL, eltnames = NULL)
 }
 \arguments{
-\item{input}{a list of objects to coerce into a list}
+\item{x.names}{a character vector of object names to coerce into a list.}
 
-\item{eltnames}{a character list, the names of the elements in the list.}
+\item{eltnames}{a character vector, the names of the elements in the list.}
 }
 \value{
 a list
@@ -23,4 +23,6 @@ the names of the elements in the output list.
 }
 \author{
 Gaye, A.
+
+Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 }
diff --git a/man/replaceNaDS.Rd b/man/replaceNaDS.Rd
index e44285bc..f6e26ed2 100644
--- a/man/replaceNaDS.Rd
+++ b/man/replaceNaDS.Rd
@@ -4,10 +4,10 @@
 \alias{replaceNaDS}
 \title{Replaces the missing values in a vector}
 \usage{
-replaceNaDS(xvect, replacements)
+replaceNaDS(x, replacements)
 }
 \arguments{
-\item{xvect}{a character, the name of the vector to process.}
+\item{x}{a character, the name of the vector to process.}
 
 \item{replacements}{a vector which contains the replacement value(s), a vector one or 
 more values for each study.}

From 713983f30b7dcfd05cca8be3b328165be5206bdd Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 16 Apr 2026 19:47:17 +0200
Subject: [PATCH 8/8] docs: updated authorship

---
 R/BooleDS.R            | 1 +
 R/cbindDS.R            | 1 +
 R/dataFrameDS.R        | 1 +
 R/dataFrameFillDS.R    | 1 +
 R/dataFrameSortDS.R    | 1 +
 R/dataFrameSubsetDS1.R | 1 +
 R/dataFrameSubsetDS2.R | 1 +
 R/mergeDS.R            | 1 +
 R/rbindDS.R            | 1 +
 R/recodeValuesDS.R     | 1 +
 R/repDS.R              | 1 +
 R/replaceNaDS.R        | 1 +
 R/seqDS.R              | 1 +
 R/unListDS.R           | 1 +
 14 files changed, 14 insertions(+)

diff --git a/R/BooleDS.R b/R/BooleDS.R
index b7e48490..7081e32a 100644
--- a/R/BooleDS.R
+++ b/R/BooleDS.R
@@ -21,6 +21,7 @@
 #' input vector are all converted to 1 or 0 respectively.
 #' 
 #' @author DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' 
 #' @return the levels of the input variable.
 #' @export
diff --git a/R/cbindDS.R b/R/cbindDS.R
index e0ad0b4c..c8717a2c 100644
--- a/R/cbindDS.R
+++ b/R/cbindDS.R
@@ -19,6 +19,7 @@
 #' of \code{ds.cbind} (or default name \code{cbind.newobj})
 #' which is written to the serverside. The output object is of class data.frame.
 #' @author Paul Burton and Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 cbindDS <- function(x.names.transmit=NULL, colnames.transmit=NULL){
diff --git a/R/dataFrameDS.R b/R/dataFrameDS.R
index 7f45c1af..611bb1a8 100644
--- a/R/dataFrameDS.R
+++ b/R/dataFrameDS.R
@@ -35,6 +35,7 @@
 #' serverside and named according to the <newobj> argument of the clientside
 #' function ds.dataFrame()
 #' @author DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 dataFrameDS <- function(vectors=NULL, r.names=NULL, ch.rows=FALSE, ch.names=TRUE, clnames=NULL, strAsFactors=TRUE, completeCases=FALSE){
diff --git a/R/dataFrameFillDS.R b/R/dataFrameFillDS.R
index 7f8d404a..7de8d805 100644
--- a/R/dataFrameFillDS.R
+++ b/R/dataFrameFillDS.R
@@ -17,6 +17,7 @@
 #' The classes supported are 'numeric', 'integer', 'character', 'factor' and 'logical'.
 #' @return Nothing is returned to the client. The generated object is written to the serverside.
 #' @author Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 dataFrameFillDS <- function(df.name, allNames.transmit, class.vect.transmit, levels.vec.transmit){
diff --git a/R/dataFrameSortDS.R b/R/dataFrameSortDS.R
index ec7f5e97..9801d804 100644
--- a/R/dataFrameSortDS.R
+++ b/R/dataFrameSortDS.R
@@ -30,6 +30,7 @@
 #' R environment as a data.frame named according to the <newobj> argument(or with
 #' default name 'dataframesort.newobj') if no name is specified
 #' @author Paul Burton, with critical error identification by
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' Leire Abarrategui-Martinez, for DataSHIELD Development Team, 2/4/2020
 #' @export
 #'
diff --git a/R/dataFrameSubsetDS1.R b/R/dataFrameSubsetDS1.R
index 1c76c1ca..5f5e0c52 100644
--- a/R/dataFrameSubsetDS1.R
+++ b/R/dataFrameSubsetDS1.R
@@ -45,6 +45,7 @@
 #' In consequence, it records error messages as studysideMessages which can only be
 #' retrieved using ds.message
 #' @author Paul Burton
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 dataFrameSubsetDS1 <- function(df.name=NULL,V1.name=NULL,V2.name=NULL,Boolean.operator.n=NULL,keep.cols=NULL,rm.cols=NULL,keep.NAs=NULL){
diff --git a/R/dataFrameSubsetDS2.R b/R/dataFrameSubsetDS2.R
index 8a9a6ed6..ff1f2bee 100644
--- a/R/dataFrameSubsetDS2.R
+++ b/R/dataFrameSubsetDS2.R
@@ -54,6 +54,7 @@
 #' without problems no studysideMessage will have been saved and ds.message("newobj")
 #' will return the message: "ALL OK: there are no studysideMessage(s) on this datasource".
 #' @author DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 dataFrameSubsetDS2<-function(df.name=NULL,V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL,keep.cols=NULL, rm.cols=NULL, keep.NAs=NULL){
diff --git a/R/mergeDS.R b/R/mergeDS.R
index 750cb3c9..2cc6a2c8 100644
--- a/R/mergeDS.R
+++ b/R/mergeDS.R
@@ -51,6 +51,7 @@
 #' without problems no studysideMessage will have been saved and ds.message(<newobj>)
 #' will return the message: "ALL OK: there are no studysideMessage(s) on this datasource".
 #' @author Paul Burton, Demetris Avraam, for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 mergeDS <- function(x.name, y.name, by.x.names.transmit, by.y.names.transmit, all.x, all.y,
 			 sort, suffixes.transmit, no.dups, incomparables){
diff --git a/R/rbindDS.R b/R/rbindDS.R
index 5b0f6764..131b863c 100644
--- a/R/rbindDS.R
+++ b/R/rbindDS.R
@@ -32,6 +32,7 @@
 #' without problems no studysideMessage will have been saved and ds.message("<newobj>")
 #' will return the message: "ALL OK: there are no studysideMessage(s) on this datasource".
 #' @author Paul Burton for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 rbindDS<-function(x.names.transmit=NULL,colnames.transmit=NULL){
   
diff --git a/R/recodeValuesDS.R b/R/recodeValuesDS.R
index 73e57279..20017d38 100644
--- a/R/recodeValuesDS.R
+++ b/R/recodeValuesDS.R
@@ -26,6 +26,7 @@
 #' initially specified in calling ds.recodeValues. The output object (the required
 #' recoded variable called <newobj> is written to the serverside.
 #' @author Paul Burton, Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 recodeValuesDS <- function(var.name.text=NULL, values2replace.text=NULL, new.values.text=NULL, missing=NULL){
diff --git a/R/repDS.R b/R/repDS.R
index f6454ea2..994d4d22 100644
--- a/R/repDS.R
+++ b/R/repDS.R
@@ -88,6 +88,7 @@
 #' without problems no studysideMessage will have been saved and ds.message("newobj")
 #' will return the message: "ALL OK: there are no studysideMessage(s) on this datasource".
 #' @author Paul Burton for DataSHIELD Development Team, 14/10/2019
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #'
 repDS <- function(x1.transmit, times.transmit, length.out.transmit, each.transmit,
diff --git a/R/replaceNaDS.R b/R/replaceNaDS.R
index 698fc018..62b91f99 100644
--- a/R/replaceNaDS.R
+++ b/R/replaceNaDS.R
@@ -13,6 +13,7 @@
 #' more values for each study. 
 #' @return a new vector without missing values
 #' @author Amadou Gaye, Demetris Avraam for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 replaceNaDS <- function(x, replacements){
diff --git a/R/seqDS.R b/R/seqDS.R
index e8af69aa..56113e4a 100644
--- a/R/seqDS.R
+++ b/R/seqDS.R
@@ -45,6 +45,7 @@
 #' without problems no studysideMessage will have been saved and ds.message("<newobj>")
 #' will return the message: "ALL OK: there are no studysideMessage(s) on this datasource".
 #' @author Paul Burton for DataSHIELD Development Team, 17/9/2019
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 seqDS <- function(FROM.value.char,TO.value.char,BY.value.char,LENGTH.OUT.value.char,ALONG.WITH.name)
 {
diff --git a/R/unListDS.R b/R/unListDS.R
index 9b620491..be0130b1 100644
--- a/R/unListDS.R
+++ b/R/unListDS.R
@@ -31,6 +31,7 @@
 #' function - one should check as far as one can
 #' the nature of the output from a call to ds.unList - e.g. ds.class, ds.length etc
 #' @author Amadou Gaye (2016), Paul Burton (19/09/2019) for DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' 
 unListDS <- function(x.name) {