From 56b1b45a1d3758403634b0490c7e3aa7687fbd4e Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:35:19 +0200 Subject: [PATCH 01/22] Add serverside checks for class and object existence --- R/colnamesDS.R | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/R/colnamesDS.R b/R/colnamesDS.R index eb1bffb9..3ffe40a4 100644 --- a/R/colnamesDS.R +++ b/R/colnamesDS.R @@ -8,15 +8,10 @@ #' @export #' colnamesDS <- function(x){ - - x.val <- eval(parse(text=x), envir = parent.frame()) - - # find the dim of the input dataframe or matrix + x.val <- .load_serverside_object(x) + .check_class(obj = x.val, obj_name = x, permitted_classes = c("data.frame", "matrix")) out <- colnames(x.val) - - # return the dimension return(out) - } #AGGREGATE FUNCTION # colnamesDS From 4a9df9f3f88d37e48e9ac7c90931c92cce0eff25 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:36:18 +0200 Subject: [PATCH 02/22] add functions in helper file --- R/utils.R | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 R/utils.R diff --git a/R/utils.R b/R/utils.R new file mode 100644 index 00000000..12304bfb --- /dev/null +++ b/R/utils.R @@ -0,0 +1,42 @@ +#' Load a Server-Side Object by Name +#' +#' Evaluates a character string referring to an object name and returns the corresponding +#' object from the parent environment. If the object does not exist, an error is raised. +#' +#' @param x A character string naming the object to be retrieved. +#' @return The evaluated R object referred to by `x`. +#' @noRd +.load_serverside_object <- function(x) { + tryCatch( + eval(parse(text = x), envir = parent.frame()), + error = function(e) { + stop("The server-side object", " '", x, "' ", "does not exist") + } + ) +} + +#' Check Class of a Server-Side Object +#' +#' Verifies that a given object is of an allowed class. If not, raises an informative error +#' message listing the permitted classes and the actual class of the object. +#' +#' @param obj The object whose class should be checked. +#' @param obj_name A character string with the name of the object (used in error messages). +#' @param permitted_classes A character vector of allowed class names. +#' +#' @return Invisibly returns `TRUE` if the class check passes; otherwise throws an error. +#' @noRd +.check_class <- function(obj, obj_name, permitted_classes) { + typ <- class(obj) + + if (!any(permitted_classes %in% typ)) { + msg <- glue( + "The server-side object must be of type {paste(permitted_classes, collapse = ' or ')}. ", + "'{obj_name}' is type {typ}." + ) + + stop(msg, call. = FALSE) + } + + invisible(TRUE) +} From 3280cd16dfc9c7001bd7424253820ad42263fb82 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:46:13 +0200 Subject: [PATCH 03/22] ran check, added dependencies --- DESCRIPTION | 3 ++- NAMESPACE | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d00d8a10..80344b1b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -71,7 +71,8 @@ Imports: gamlss, gamlss.dist, mice, - childsds + childsds, + glue Suggests: spelling, testthat diff --git a/NAMESPACE b/NAMESPACE index 897148d1..db4a5378 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -140,3 +140,5 @@ import(gamlss.dist) import(mice) importFrom(gamlss.dist,pST3) importFrom(gamlss.dist,qST3) +importFrom(glue,glue) +importFrom(glue,glue_collapse) From cee9a8126898099bf1993263d45fa0404955bc01 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:46:34 +0200 Subject: [PATCH 04/22] just use glue within messages for consistency --- R/utils.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/utils.R b/R/utils.R index 12304bfb..3103e010 100644 --- a/R/utils.R +++ b/R/utils.R @@ -23,7 +23,7 @@ #' @param obj The object whose class should be checked. #' @param obj_name A character string with the name of the object (used in error messages). #' @param permitted_classes A character vector of allowed class names. -#' +#' @importFrom glue glue glue_collapse #' @return Invisibly returns `TRUE` if the class check passes; otherwise throws an error. #' @noRd .check_class <- function(obj, obj_name, permitted_classes) { @@ -31,7 +31,7 @@ if (!any(permitted_classes %in% typ)) { msg <- glue( - "The server-side object must be of type {paste(permitted_classes, collapse = ' or ')}. ", + "The server-side object must be of type {glue_collapse(permitted_classes, sep = ' or ')}. ", "'{obj_name}' is type {typ}." ) From 29d73aadf2da34878f7b7409a167ddda695ef4ae Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:54:23 +0200 Subject: [PATCH 05/22] renamed snake case to camel case to match naming convention --- R/colnamesDS.R | 4 ++-- R/utils.R | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/colnamesDS.R b/R/colnamesDS.R index 3ffe40a4..6dc2e99e 100644 --- a/R/colnamesDS.R +++ b/R/colnamesDS.R @@ -8,8 +8,8 @@ #' @export #' colnamesDS <- function(x){ - x.val <- .load_serverside_object(x) - .check_class(obj = x.val, obj_name = x, permitted_classes = c("data.frame", "matrix")) + x.val <- .loadServersideObject(x) + .checkClass(obj = x.val, obj_name = x, permitted_classes = c("data.frame", "matrix")) out <- colnames(x.val) return(out) } diff --git a/R/utils.R b/R/utils.R index 3103e010..8910dbf9 100644 --- a/R/utils.R +++ b/R/utils.R @@ -6,7 +6,7 @@ #' @param x A character string naming the object to be retrieved. #' @return The evaluated R object referred to by `x`. #' @noRd -.load_serverside_object <- function(x) { +.loadServersideObject <- function(x) { tryCatch( eval(parse(text = x), envir = parent.frame()), error = function(e) { @@ -26,7 +26,7 @@ #' @importFrom glue glue glue_collapse #' @return Invisibly returns `TRUE` if the class check passes; otherwise throws an error. #' @noRd -.check_class <- function(obj, obj_name, permitted_classes) { +.checkClass <- function(obj, obj_name, permitted_classes) { typ <- class(obj) if (!any(permitted_classes %in% typ)) { From 245bbbabf8d2058f69aef6539792770b9713d36c Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 13:05:00 +0200 Subject: [PATCH 06/22] require testthat version 3 --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 80344b1b..44b879c2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -75,7 +75,8 @@ Imports: glue Suggests: spelling, - testthat + testthat (>= 3.0.0) RoxygenNote: 7.3.3 Encoding: UTF-8 Language: en-GB +Config/testthat/edition: 3 From 01b0f0feb6fb2977cd85e570e4614be14906aa49 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 13:05:14 +0200 Subject: [PATCH 07/22] test: unit tests for helper files --- tests/testthat/test-smk-utils.R | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 tests/testthat/test-smk-utils.R diff --git a/tests/testthat/test-smk-utils.R b/tests/testthat/test-smk-utils.R new file mode 100644 index 00000000..de901962 --- /dev/null +++ b/tests/testthat/test-smk-utils.R @@ -0,0 +1,46 @@ + +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of 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 . +#------------------------------------------------------------------------------- + +# +# Set up +# + +context("utils::smk::setup") +test_that(".loadServersideObject() returns existing object", { + test_df <- data.frame(a = 1:3) + result <- .loadServersideObject("test_df") + expect_identical(result, test_df) +}) + +test_that(".loadServersideObject() throws error for missing object", { + expect_error( + .loadServersideObject("nonexistent_obj"), + regexp = "does not exist" + ) +}) + +test_that(".checkClass() passes for correct class", { + df <- data.frame(a = 1) + expect_invisible( + .checkClass(df, "df", c("data.frame", "matrix")) + ) +}) + +test_that(".checkClass() throws informative error for wrong class", { + x <- list(a = 1) + expect_error( + .checkClass(x, "x", c("data.frame", "matrix")), + regexp = "must be of type data.frame or matrix" + ) +}) + +context("utils::smk::shutdown") +context("utils::smk::done") From 4a1721264a70ca97c8b403452fddbda74fae5237 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 13:14:02 +0200 Subject: [PATCH 08/22] look in correct environment, ie 2 steps up --- R/utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index 8910dbf9..6fd53936 100644 --- a/R/utils.R +++ b/R/utils.R @@ -8,7 +8,7 @@ #' @noRd .loadServersideObject <- function(x) { tryCatch( - eval(parse(text = x), envir = parent.frame()), + eval(parse(text = x), envir = parent.frame(2)), error = function(e) { stop("The server-side object", " '", x, "' ", "does not exist") } From 677173166dae22d4094d853e081d30c2f1b172c2 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 13:14:24 +0200 Subject: [PATCH 09/22] write unit tests for unhappy path --- tests/testthat/test-smk-colnamesDS.R | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/tests/testthat/test-smk-colnamesDS.R b/tests/testthat/test-smk-colnamesDS.R index 2c4d3e3c..689cc2f3 100644 --- a/tests/testthat/test-smk-colnamesDS.R +++ b/tests/testthat/test-smk-colnamesDS.R @@ -42,10 +42,24 @@ test_that("simple colnamesDS, data.matrix", { expect_true("v2" %in% res) }) +test_that("colnamesDS throws error when object does not exist", { + expect_error( + colnamesDS("nonexistent_object"), + regexp = "does not exist" + ) +}) + +test_that("colnamesDS throws error when object is not data.frame or matrix", { + bad_input <- list(a = 1:3, b = 4:6) + expect_error( + colnamesDS("bad_input"), + regexp = "must be of type data.frame or matrix" + ) +}) + # # Done # context("colnamesDS::smk::shutdown") - context("colnamesDS::smk::done") From c5e961ee0434f6bbe9865c9776aa2aa98b588271 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 9 Oct 2025 14:57:11 +0200 Subject: [PATCH 10/22] added template with checklist for PRs --- pull_request_template | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 pull_request_template diff --git a/pull_request_template b/pull_request_template new file mode 100644 index 00000000..561614a9 --- /dev/null +++ b/pull_request_template @@ -0,0 +1,15 @@ +## Description +[Write a description of the changes you have made] + +## Checklist (all items may not apply) + +### Refactor +- [ ] Replace `eval(parse(text = x), envir = parent.frame())` with `.loadServersideObject()` +- [ ] Where appropriate, check object class using `.checkClass() +- [ ] Check whether additional checks are required on the server-side + +### Testing +- [ ] Writen server-side unit tests for unhappy flow +- [ ] Run and passed `devtools::test(filter = "smk-|disc|arg")` +- [ ] Run and passed `devtools::check(args = '--no-tests')` (we run tests separately to skip performance checks) +- [ ] Run and passed `devtools::build` From cc8d8f8fbf0dc00dc46280c6076694f610b62de2 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 21 Oct 2025 11:21:36 +0100 Subject: [PATCH 11/22] Added 'pull_request_template' --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 59863e10..26e4d4d4 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,3 +11,4 @@ ^\.circleci/config\.yml$ ^\.github$ ^cran-comments\.md$ +^pull_request_template$ From aa9fb8f1005801b35e989bee3727762253e36b4d Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Sun, 26 Oct 2025 19:32:40 +0000 Subject: [PATCH 12/22] Updates for context() + copyright --- .../perf_files/default_perf_profile.csv | 8 ++--- tests/testthat/perf_files/hp-laptop_quay.csv | 8 ++--- tests/testthat/setup.R | 5 +-- tests/testthat/teardown.R | 5 +-- tests/testthat/test-arg-asIntegerDS.R | 10 +++--- tests/testthat/test-arg-asLogicalDS.R | 13 +++---- tests/testthat/test-arg-dataFrameFillDS.R | 9 ++--- tests/testthat/test-arg-dataFrameSortDS.R | 9 ++--- tests/testthat/test-arg-uniqueDS.R | 15 ++++---- tests/testthat/test-disc-meanDS.R | 9 ++--- tests/testthat/test-disc-varDS.R | 9 ++--- tests/testthat/test-perf-meanDS.R | 12 +++---- tests/testthat/test-perf-varDS.R | 12 +++---- tests/testthat/test-smk-BooleDS.R | 23 ++++++------ tests/testthat/test-smk-absDS.R | 19 +++++----- tests/testthat/test-smk-asCharacterDS.R | 15 ++++---- tests/testthat/test-smk-asDataMatrixDS.R | 9 ++--- tests/testthat/test-smk-asFactorDS1.R | 9 ++--- tests/testthat/test-smk-asFactorDS2.R | 8 ++--- tests/testthat/test-smk-asFactorSimpleDS.R | 9 ++--- tests/testthat/test-smk-asIntegerDS.R | 15 ++++---- tests/testthat/test-smk-asListDS.R | 9 ++--- tests/testthat/test-smk-asLogicalDS.R | 17 ++++----- tests/testthat/test-smk-asMatrixDS.R | 9 ++--- tests/testthat/test-smk-asNumericDS.R | 35 ++++++++++--------- tests/testthat/test-smk-aucDS.R | 7 ++-- tests/testthat/test-smk-bp_standardsDS.R | 11 +++--- tests/testthat/test-smk-cDS.R | 15 ++++---- tests/testthat/test-smk-cbindDS.R | 9 ++--- tests/testthat/test-smk-changeRefGroupDS.R | 9 ++--- tests/testthat/test-smk-checkNegValueDS.R | 11 +++--- tests/testthat/test-smk-classDS.R | 33 ++++++++--------- tests/testthat/test-smk-colnamesDS.R | 11 +++--- tests/testthat/test-smk-completeCasesDS.R | 15 ++++---- tests/testthat/test-smk-corDS.R | 15 ++++---- tests/testthat/test-smk-corTestDS.R | 19 +++++----- tests/testthat/test-smk-covDS.R | 11 +++--- tests/testthat/test-smk-dataFrameDS.R | 9 ++--- tests/testthat/test-smk-dataFrameFillDS.R | 10 +++--- tests/testthat/test-smk-dataFrameSortDS.R | 11 +++--- tests/testthat/test-smk-dataFrameSubsetDS1.R | 11 +++--- tests/testthat/test-smk-dataFrameSubsetDS2.R | 11 +++--- tests/testthat/test-smk-densityGridDS.R | 9 ++--- tests/testthat/test-smk-dimDS.R | 11 +++--- tests/testthat/test-smk-extract.R | 11 +++--- tests/testthat/test-smk-gamlssDS.R | 9 ++--- tests/testthat/test-smk-getWGSRDS.R | 9 ++--- tests/testthat/test-smk-hetcorDS.R | 9 ++--- tests/testthat/test-smk-igb_standardsDS.R | 9 ++--- tests/testthat/test-smk-isNaDS.R | 11 +++--- tests/testthat/test-smk-isValidDS.R | 33 ++++++++--------- tests/testthat/test-smk-kurtosisDS1.R | 13 +++---- tests/testthat/test-smk-kurtosisDS2.R | 9 ++--- tests/testthat/test-smk-lengthDS.R | 11 +++--- tests/testthat/test-smk-levelsDS.R | 9 ++--- tests/testthat/test-smk-listDS.R | 9 ++--- .../test-smk-listDisclosureSettingsDS.R | 9 ++--- tests/testthat/test-smk-lsDS.R | 11 +++--- tests/testthat/test-smk-meanDS.R | 13 +++---- tests/testthat/test-smk-messageDS.R | 9 ++--- tests/testthat/test-smk-metadataDS.R | 12 +++---- tests/testthat/test-smk-miceDS.R | 9 ++--- tests/testthat/test-smk-minMaxRandDS.R | 8 ++--- tests/testthat/test-smk-namesDS.R | 11 +++--- tests/testthat/test-smk-numNaDS.R | 9 ++--- tests/testthat/test-smk-quantileMeanDS.R | 11 +++--- tests/testthat/test-smk-rBinomDS.R | 9 ++--- tests/testthat/test-smk-rNormDS.R | 9 ++--- tests/testthat/test-smk-rPoisDS.R | 9 ++--- tests/testthat/test-smk-rUnifDS.R | 9 ++--- tests/testthat/test-smk-rangeDS.R | 11 +++--- tests/testthat/test-smk-rbindDS.R | 9 ++--- tests/testthat/test-smk-recodeLevelsDS.R | 7 ++-- tests/testthat/test-smk-recodeValuesDS.R | 7 ++-- tests/testthat/test-smk-replaceNaDS.R | 9 ++--- tests/testthat/test-smk-rmDS.R | 17 ++++----- tests/testthat/test-smk-rowColCalcDS.R | 9 ++--- tests/testthat/test-smk-sampleDS.R | 9 ++--- tests/testthat/test-smk-seqDS.R | 9 ++--- tests/testthat/test-smk-setFilterDS.R | 9 ++--- tests/testthat/test-smk-setSeedDS.R | 9 ++--- tests/testthat/test-smk-skewnessDS1.R | 13 +++---- tests/testthat/test-smk-skewnessDS2.R | 9 ++--- tests/testthat/test-smk-sqrtDS.R | 19 +++++----- tests/testthat/test-smk-subsetByClassDS.R | 9 ++--- tests/testthat/test-smk-subsetDS.R | 9 ++--- tests/testthat/test-smk-tapplyDS.R | 7 ++-- tests/testthat/test-smk-tapplyDS.assign.R | 9 ++--- tests/testthat/test-smk-testObjExistsDS.R | 35 ++++++++++--------- tests/testthat/test-smk-unListDS.R | 9 ++--- tests/testthat/test-smk-uniqueDS.R | 11 +++--- tests/testthat/test-smk-varDS.R | 13 +++---- tests/testthat/test-smk-vectorDS.R | 16 ++++----- 93 files changed, 583 insertions(+), 500 deletions(-) diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv index 77f556bc..7ab03037 100644 --- a/tests/testthat/perf_files/default_perf_profile.csv +++ b/tests/testthat/perf_files/default_perf_profile.csv @@ -1,5 +1,5 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"meanDS::perf::numeric::0","2998.9844","0.5","2" -"meanDS::perf::numberAndNA::0","3027.3963","0.5","2" -"varDS::perf::numeric::0","3124.4088","0.5","2" -"varDS::perf::numberAndNA::0","3146.532","0.5","2" +"meanDS::perf::numeric::0","11557.1204746495","0.5","2" +"meanDS::perf::numberAndNA::0","11718.8520447749","0.5","2" +"varDS::perf::numeric::0","12758.5511531009","0.5","2" +"varDS::perf::numberAndNA::0","12545.8819532662","0.5","2" diff --git a/tests/testthat/perf_files/hp-laptop_quay.csv b/tests/testthat/perf_files/hp-laptop_quay.csv index 487b248f..7ab03037 100644 --- a/tests/testthat/perf_files/hp-laptop_quay.csv +++ b/tests/testthat/perf_files/hp-laptop_quay.csv @@ -1,5 +1,5 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"meanDS::perf::numeric::0","8874.24924669612","0.5","2" -"meanDS::perf::numberAndNA::0","8946.22935183172","0.5","2" -"varDS::perf::numeric::0","10029.1022487173","0.5","2" -"varDS::perf::numberAndNA::0","10014.7789085673","0.5","2" +"meanDS::perf::numeric::0","11557.1204746495","0.5","2" +"meanDS::perf::numberAndNA::0","11718.8520447749","0.5","2" +"varDS::perf::numeric::0","12758.5511531009","0.5","2" +"varDS::perf::numberAndNA::0","12545.8819532662","0.5","2" diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index e7a0549e..c3e6b288 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -11,7 +12,7 @@ # Datashield test suite set up # -context("setup - start") +# context("setup - start") library(RANN) library(stringr) @@ -22,4 +23,4 @@ source("random/set_random_seed_settings.R") source("perf_tests/perf_rate.R") -context("setup - done") +# context("setup - done") diff --git a/tests/testthat/teardown.R b/tests/testthat/teardown.R index 2a5a788c..1088bcbe 100644 --- a/tests/testthat/teardown.R +++ b/tests/testthat/teardown.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 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. @@ -8,6 +9,6 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -context("teardown - start") +# context("teardown - start") -context("teardown - done") +# context("teardown - done") diff --git a/tests/testthat/test-arg-asIntegerDS.R b/tests/testthat/test-arg-asIntegerDS.R index 5bd6ed58..c2ebd028 100644 --- a/tests/testthat/test-arg-asIntegerDS.R +++ b/tests/testthat/test-arg-asIntegerDS.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 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. @@ -12,13 +12,13 @@ # Set up # -context("asIntegerDS::arg::setup") +# context("asIntegerDS::arg::setup") # # Tests # -context("asIntegerDS::arg::direct input numeric") +# context("asIntegerDS::arg::direct input numeric") test_that("simple asIntegerDS non-input", { expect_error(asIntegerDS(1.0), "ERROR: x.name must be specified as a character string", fixed = TRUE) }) @@ -27,6 +27,6 @@ test_that("simple asIntegerDS non-input", { # Done # -context("asIntegerDS::arg::shutdown") +# context("asIntegerDS::arg::shutdown") -context("asIntegerDS::arg::done") +# context("asIntegerDS::arg::done") diff --git a/tests/testthat/test-arg-asLogicalDS.R b/tests/testthat/test-arg-asLogicalDS.R index 7887ca74..33159504 100644 --- a/tests/testthat/test-arg-asLogicalDS.R +++ b/tests/testthat/test-arg-asLogicalDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,25 +13,25 @@ # Set up # -context("asLogicalDS::arg::setup") +# context("asLogicalDS::arg::setup") # # Tests # -context("asLogicalDS::arg::direct input numeric") +# context("asLogicalDS::arg::direct input numeric") test_that("simple asLogicalDS non-input", { expect_error(asLogicalDS(1.0), "ERROR: x.name must be specified as a character string", fixed = TRUE) }) -context("asLogicalDS::arg::input NULL") +# context("asLogicalDS::arg::input NULL") test_that("simple asLogicalDS NULL", { input <- NULL expect_error(asLogicalDS("input"), "ERROR: for ds.asLogical function, x.name must specify an input object of class numeric, integer, character or matrix", fixed = TRUE) }) -context("asLogicalDS::arg::input NA") +# context("asLogicalDS::arg::input NA") test_that("simple asLogicalDS NA", { input <- NA @@ -41,6 +42,6 @@ test_that("simple asLogicalDS NA", { # Done # -context("asLogicalDS::arg::shutdown") +# context("asLogicalDS::arg::shutdown") -context("asLogicalDS::arg::done") +# context("asLogicalDS::arg::done") diff --git a/tests/testthat/test-arg-dataFrameFillDS.R b/tests/testthat/test-arg-dataFrameFillDS.R index d11cacd8..19c710aa 100644 --- a/tests/testthat/test-arg-dataFrameFillDS.R +++ b/tests/testthat/test-arg-dataFrameFillDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("dataFrameFillDS::arg::setup") +# context("dataFrameFillDS::arg::setup") # # Tests # -context("dataFrameFillDS::arg") +# context("dataFrameFillDS::arg") test_that("simple dataFrameFillDS, ascending, numeric", { df <- data.frame(v1 = c(-2.0, -3.0, 4.0, 2.0, 1.0, 0.0, -1.0, 3.0), v2 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0)) allNames.transmit <- "v1,v2,v3,v4,v5,v6,v7" @@ -45,10 +46,10 @@ test_that("simple dataFrameFillDS, ascending, numeric", { # Shutdown # -context("dataFrameFillDS::arg::shutdown") +# context("dataFrameFillDS::arg::shutdown") # # Done # -context("dataFrameFillDS::arg::done") +# context("dataFrameFillDS::arg::done") diff --git a/tests/testthat/test-arg-dataFrameSortDS.R b/tests/testthat/test-arg-dataFrameSortDS.R index 6f193172..a720588d 100644 --- a/tests/testthat/test-arg-dataFrameSortDS.R +++ b/tests/testthat/test-arg-dataFrameSortDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("dataFrameSortDS::arg::setup") +# context("dataFrameSortDS::arg::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("dataFrameSortDS::arg") +# context("dataFrameSortDS::arg") test_that("simple dataFrameSortDS, factor error check", { df <- data.frame(v1 = as.factor(c("a", "b", "c", "d", "b", "e", "f", "f")), v2 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0)) sort.key.name <- "df$v1" @@ -34,10 +35,10 @@ test_that("simple dataFrameSortDS, factor error check", { # Shutdown # -context("dataFrameSortDS::arg::shutdown") +# context("dataFrameSortDS::arg::shutdown") # # Done # -context("dataFrameSortDS::arg::done") +# context("dataFrameSortDS::arg::done") diff --git a/tests/testthat/test-arg-uniqueDS.R b/tests/testthat/test-arg-uniqueDS.R index 1c1a1133..48d6bd48 100644 --- a/tests/testthat/test-arg-uniqueDS.R +++ b/tests/testthat/test-arg-uniqueDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,29 +13,29 @@ # Set up # -context("uniqueDS::arg::setup") +# context("uniqueDS::arg::setup") # # Tests # -context("uniqueDS::arg::simple null argument") +# context("uniqueDS::arg::simple null argument") test_that("simple uniqueDS for NULL", { expect_error(uniqueDS(NULL), "Variable's name can't be NULL", fixed = TRUE) }) -context("uniqueDS::arg::null value") +# context("uniqueDS::arg::null value") test_that("simple uniqueDS for NULL", { input <- NULL expect_error(uniqueDS("input"), "Variable can't be NULL", fixed = TRUE) }) -context("uniqueDS::arg::not character value") +# context("uniqueDS::arg::not character value") test_that("simple uniqueDS for NULL", { expect_error(uniqueDS(17), "Variable's name isn't a single character vector", fixed = TRUE) }) -context("uniqueDS::arg::missing value") +# context("uniqueDS::arg::missing value") test_that("simple uniqueDS for NULL", { expect_error(uniqueDS("input"), "object 'input' not found", fixed = TRUE) }) @@ -43,6 +44,6 @@ test_that("simple uniqueDS for NULL", { # Done # -context("uniqueDS::arg::shutdown") +# context("uniqueDS::arg::shutdown") -context("uniqueDS::arg::done") +# context("uniqueDS::arg::done") diff --git a/tests/testthat/test-disc-meanDS.R b/tests/testthat/test-disc-meanDS.R index 0d5b0ddc..22864733 100644 --- a/tests/testthat/test-disc-meanDS.R +++ b/tests/testthat/test-disc-meanDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("meanDS::disc::setup") +# context("meanDS::disc::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("meanDS::disc::numeric with below nfilter.tab values") +# context("meanDS::disc::numeric with below nfilter.tab values") test_that("numeric meanDS, with below nfilter.tab values", { input <- c(NA, NA, 2.0, NA, 4.0) @@ -31,6 +32,6 @@ test_that("numeric meanDS, with below nfilter.tab values", { # Done # -context("meanDS::disc::shutdown") +# context("meanDS::disc::shutdown") -context("meanDS::disc::done") +# context("meanDS::disc::done") diff --git a/tests/testthat/test-disc-varDS.R b/tests/testthat/test-disc-varDS.R index ed7d0384..3b60a771 100644 --- a/tests/testthat/test-disc-varDS.R +++ b/tests/testthat/test-disc-varDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("varDS::disc::setup") +# context("varDS::disc::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("varDS::disc::numeric with below nfilter.tab values") +# context("varDS::disc::numeric with below nfilter.tab values") test_that("numeric varDS, with below nfilter.tab values", { input <- c(NA, NA, 2.0, NA, 4.0) @@ -31,6 +32,6 @@ test_that("numeric varDS, with below nfilter.tab values", { # Done # -context("varDS::disc::shutdown") +# context("varDS::disc::shutdown") -context("varDS::disc::done") +# context("varDS::disc::done") diff --git a/tests/testthat/test-perf-meanDS.R b/tests/testthat/test-perf-meanDS.R index 794e61b2..4cee2473 100644 --- a/tests/testthat/test-perf-meanDS.R +++ b/tests/testthat/test-perf-meanDS.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 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. @@ -16,7 +16,7 @@ testthat::skip_on_cran() testthat::skip_on_ci() -context("meanDS::perf::setup") +# context("meanDS::perf::setup") set.standard.disclosure.settings() @@ -24,7 +24,7 @@ set.standard.disclosure.settings() # Tests # -context("meanDS::perf::numeric") +# context("meanDS::perf::numeric") test_that("numeric meanDS - performance", { skip_on_cran() @@ -59,7 +59,7 @@ test_that("numeric meanDS - performance", { expect_lt(.current.rate, .reference.rate * .reference.tolerance.upper, label = "Observed rate", expected.label = "upper threshold on rate") }) -context("meanDS::perf::numeric with NA") +# context("meanDS::perf::numeric with NA") test_that("numeric meanDS, with NA - performance", { skip_on_cran() @@ -98,6 +98,6 @@ test_that("numeric meanDS, with NA - performance", { # Done # -context("meanDS::perf::shutdown") +# context("meanDS::perf::shutdown") -context("meanDS::perf::done") +# context("meanDS::perf::done") diff --git a/tests/testthat/test-perf-varDS.R b/tests/testthat/test-perf-varDS.R index d468c5da..459e6f03 100644 --- a/tests/testthat/test-perf-varDS.R +++ b/tests/testthat/test-perf-varDS.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 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. @@ -16,7 +16,7 @@ testthat::skip_on_cran() testthat::skip_on_ci() -context("varDS::perf::setup") +# context("varDS::perf::setup") set.standard.disclosure.settings() @@ -24,7 +24,7 @@ set.standard.disclosure.settings() # Tests # -context("varDS::perf::numeric") +# context("varDS::perf::numeric") test_that("numeric varDS - performance", { skip_on_cran() @@ -59,7 +59,7 @@ test_that("numeric varDS - performance", { expect_lt(.current.rate, .reference.rate * .reference.tolerance.upper, label = "Observed rate", expected.label = "upper threshold on rate") }) -context("varDS::perf::numeric with NA") +# context("varDS::perf::numeric with NA") test_that("numeric varDS, with NA - performance", { skip_on_cran() @@ -98,6 +98,6 @@ test_that("numeric varDS, with NA - performance", { # Done # -context("varDS::perf::shutdown") +# context("varDS::perf::shutdown") -context("varDS::perf::done") +# context("varDS::perf::done") diff --git a/tests/testthat/test-smk-BooleDS.R b/tests/testthat/test-smk-BooleDS.R index dd10c782..5fcfa4ee 100644 --- a/tests/testthat/test-smk-BooleDS.R +++ b/tests/testthat/test-smk-BooleDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("BooleDS::smk::setup") +# context("BooleDS::smk::setup") # # Tests # -context("BooleDS::smk::simple equal") +# context("BooleDS::smk::simple equal") test_that("simple BooleDS, equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -47,7 +48,7 @@ test_that("simple BooleDS, equal logical", { expect_equal(res[5], FALSE) }) -context("BooleDS::smk::simple not-equal") +# context("BooleDS::smk::simple not-equal") test_that("simple BooleDS, not-equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -76,7 +77,7 @@ test_that("simple BooleDS, not-equal logical", { expect_equal(res[5], TRUE) }) -context("BooleDS::smk::simple less-than") +# context("BooleDS::smk::simple less-than") test_that("simple BooleDS, less-than numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -105,7 +106,7 @@ test_that("simple BooleDS, less-than logical", { expect_equal(res[5], FALSE) }) -context("BooleDS::smk::simple less-than-equal") +# context("BooleDS::smk::simple less-than-equal") test_that("simple BooleDS, less-than-equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -134,7 +135,7 @@ test_that("simple BooleDS, less-than-equal logical", { expect_equal(res[5], FALSE) }) -context("BooleDS::smk::simple greater-than") +# context("BooleDS::smk::simple greater-than") test_that("simple BooleDS, greater-than numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -163,7 +164,7 @@ test_that("simple BooleDS, greater-than logical", { expect_equal(res[5], TRUE) }) -context("BooleDS::smk::simple greater-than-equal") +# context("BooleDS::smk::simple greater-than-equal") test_that("simple BooleDS, greater-than-equal numeric", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -192,7 +193,7 @@ test_that("simple BooleDS, greater-than-equal logical", { expect_equal(res[5], TRUE) }) -context("BooleDS::smk::na-check numeric") +# context("BooleDS::smk::na-check numeric") test_that("na-check BooleDS, numeric, NA=NA", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) @@ -235,7 +236,7 @@ test_that("na-check BooleDS, numeric, NA=1", { expect_equal(res[5], 1) }) -context("BooleDS::smk::na-check logical") +# context("BooleDS::smk::na-check logical") test_that("na-check BooleDS, logical, NA=NA", { input <- data.frame(v1 = c(0.0, NA, 2.0, 3.0, NA), v2 = c(NA, 3.0, 2.0, 1.0, NA)) @@ -282,6 +283,6 @@ test_that("na-check BooleDS, logical, NA=1", { # Done # -context("BooleDS::smk::shutdown") +# context("BooleDS::smk::shutdown") -context("BooleDS::smk::done") +# context("BooleDS::smk::done") diff --git a/tests/testthat/test-smk-absDS.R b/tests/testthat/test-smk-absDS.R index c9c1cca9..54655c99 100644 --- a/tests/testthat/test-smk-absDS.R +++ b/tests/testthat/test-smk-absDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("absDS::smk::setup") +# context("absDS::smk::setup") # # Tests # -context("absDS::smk::special") +# context("absDS::smk::special") test_that("simple absDS, NA", { input <- NA @@ -59,7 +60,7 @@ test_that("simple absDS, -Inf", { expect_true(is.infinite(res)) }) -context("absDS::smk::numeric") +# context("absDS::smk::numeric") test_that("simple absDS, numeric 0.0", { input <- 0.0 @@ -90,7 +91,7 @@ test_that("simple absDS, numeric -10.0", { expect_equal(res, 10.0) }) -context("absDS::smk::integer") +# context("absDS::smk::integer") test_that("simple absDS, integer 0L", { input <- 0L @@ -121,7 +122,7 @@ test_that("simple absDS, integer -10L", { expect_equal(res, 10L) }) -context("absDS::smk::special vector") +# context("absDS::smk::special vector") test_that("simple absDS", { input <- c(NA, NaN, Inf, -Inf) @@ -135,7 +136,7 @@ test_that("simple absDS", { expect_true(is.infinite(res[4])) }) -context("absDS::smk::numeric vector") +# context("absDS::smk::numeric vector") test_that("simple absDS", { input <- c(0.0, 4.0, 9.0, -10.0, -50.0, -20.0) @@ -151,7 +152,7 @@ test_that("simple absDS", { expect_equal(res[6], 20.0) }) -context("absDS::smk::integer vector") +# context("absDS::smk::integer vector") test_that("simple absDS", { input <- c(0L, 4L, 9L, -10L, -50L, -20L) @@ -171,6 +172,6 @@ test_that("simple absDS", { # Done # -context("absDS::smk::shutdown") +# context("absDS::smk::shutdown") -context("absDS::smk::done") +# context("absDS::smk::done") diff --git a/tests/testthat/test-smk-asCharacterDS.R b/tests/testthat/test-smk-asCharacterDS.R index a37c7a82..40cdaf73 100644 --- a/tests/testthat/test-smk-asCharacterDS.R +++ b/tests/testthat/test-smk-asCharacterDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("asCharacterDS::smk::setup") +# context("asCharacterDS::smk::setup") # # Tests # -context("asCharacterDS::smk::numeric") +# context("asCharacterDS::smk::numeric") test_that("numeric asCharacterDS", { input <- 3.141 @@ -29,7 +30,7 @@ test_that("numeric asCharacterDS", { expect_equal(res, "3.141") }) -context("asCharacterDS::smk::numeric vector") +# context("asCharacterDS::smk::numeric vector") test_that("numeric vector asCharacterDS", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) @@ -44,7 +45,7 @@ test_that("numeric vector asCharacterDS", { expect_equal(res[5], "4") }) -context("asCharacterDS::smk::logical") +# context("asCharacterDS::smk::logical") test_that("logical asCharacterDS - FALSE", { input <- FALSE @@ -65,7 +66,7 @@ test_that("logical asCharacterDS - TRUE", { expect_equal(res, "TRUE") }) -context("asCharacterDS::smk::logical vector") +# context("asCharacterDS::smk::logical vector") test_that("logical vector asCharacterDS", { input <- c(TRUE, FALSE, TRUE, FALSE, TRUE) @@ -84,6 +85,6 @@ test_that("logical vector asCharacterDS", { # Done # -context("asCharacterDS::smk::shutdown") +# context("asCharacterDS::smk::shutdown") -context("asCharacterDS::smk::done") +# context("asCharacterDS::smk::done") diff --git a/tests/testthat/test-smk-asDataMatrixDS.R b/tests/testthat/test-smk-asDataMatrixDS.R index 6c4f567c..eaed9318 100644 --- a/tests/testthat/test-smk-asDataMatrixDS.R +++ b/tests/testthat/test-smk-asDataMatrixDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("asDataMatrixDS::smk::setup") +# context("asDataMatrixDS::smk::setup") # # Tests # -context("asDataMatrixDS::smk::simple") +# context("asDataMatrixDS::smk::simple") test_that("simple asDataMatrixDS", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -59,6 +60,6 @@ test_that("simple asDataMatrixDS", { # Done # -context("asDataMatrixDS::smk::shutdown") +# context("asDataMatrixDS::smk::shutdown") -context("asDataMatrixDS::smk::done") +# context("asDataMatrixDS::smk::done") diff --git a/tests/testthat/test-smk-asFactorDS1.R b/tests/testthat/test-smk-asFactorDS1.R index fd59cefc..a990d4ff 100644 --- a/tests/testthat/test-smk-asFactorDS1.R +++ b/tests/testthat/test-smk-asFactorDS1.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("asFactorDS1::smk::setup") +# context("asFactorDS1::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("asFactorDS1::smk::simple") +# context("asFactorDS1::smk::simple") test_that("simple asFactorDS1", { input <- c(2.0, 1.0, 3.0, 3.0, 3.0, 1.0, 2.0, 2.0, 1.0, 2.0) @@ -37,6 +38,6 @@ test_that("simple asFactorDS1", { # Done # -context("asFactorDS1::smk::shutdown") +# context("asFactorDS1::smk::shutdown") -context("asFactorDS1::smk::done") +# context("asFactorDS1::smk::done") diff --git a/tests/testthat/test-smk-asFactorDS2.R b/tests/testthat/test-smk-asFactorDS2.R index db4a3876..1c761d4d 100644 --- a/tests/testthat/test-smk-asFactorDS2.R +++ b/tests/testthat/test-smk-asFactorDS2.R @@ -12,7 +12,7 @@ # Set up # -context("asFactorDS2::smk::setup") +# context("asFactorDS2::smk::setup") set.standard.disclosure.settings() @@ -20,7 +20,7 @@ set.standard.disclosure.settings() # Tests # -context("asFactorDS2::smk::simple") +# context("asFactorDS2::smk::simple") test_that("simple asFactorDS2, fixed.dummy.vars is FALSE", { input <- c(2, 1, 3, 3, 3, 1, 2, 2, 1, 2) all.unique.levels.transmit <- "1,2,3,4" @@ -113,6 +113,6 @@ test_that("simple asFactorDS2, fixed.dummy.vars is TRUE", { # Done # -context("asFactorDS2::smk::shutdown") +# context("asFactorDS2::smk::shutdown") -context("asFactorDS2::smk::done") +# context("asFactorDS2::smk::done") diff --git a/tests/testthat/test-smk-asFactorSimpleDS.R b/tests/testthat/test-smk-asFactorSimpleDS.R index bafe51b3..dd5a17dc 100644 --- a/tests/testthat/test-smk-asFactorSimpleDS.R +++ b/tests/testthat/test-smk-asFactorSimpleDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("asFactorSimpleDS::smk::setup") +# context("asFactorSimpleDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("asFactorSimpleDS::smk::simple") +# context("asFactorSimpleDS::smk::simple") test_that("simple asFactorSimpleDS", { input <- c(2.0, 1.0, 3.0, 3.0, 3.0, 1.0, 2.0, 2.0, 1.0, 2.0) @@ -52,6 +53,6 @@ test_that("simple asFactorSimpleDS", { # Done # -context("asFactorSimpleDS::smk::shutdown") +# context("asFactorSimpleDS::smk::shutdown") -context("asFactorSimpleDS::smk::done") +# context("asFactorSimpleDS::smk::done") diff --git a/tests/testthat/test-smk-asIntegerDS.R b/tests/testthat/test-smk-asIntegerDS.R index 902bc198..2ed33a33 100644 --- a/tests/testthat/test-smk-asIntegerDS.R +++ b/tests/testthat/test-smk-asIntegerDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("asIntegerDS::smk::setup") +# context("asIntegerDS::smk::setup") # # Tests # -context("asIntegerDS::smk::numeric") +# context("asIntegerDS::smk::numeric") test_that("numeric asIntegerDS", { input <- 3.141 @@ -29,7 +30,7 @@ test_that("numeric asIntegerDS", { expect_equal(res, 3) }) -context("asIntegerDS::smk::numeric vector") +# context("asIntegerDS::smk::numeric vector") test_that("numeric vector asIntegerDS", { input <- c(0.1, 1.1, 2.1, 3.1, 4.1) @@ -44,7 +45,7 @@ test_that("numeric vector asIntegerDS", { expect_equal(res[5], 4) }) -context("asIntegerDS::smk::character") +# context("asIntegerDS::smk::character") test_that("character asIntegerDS - FALSE", { input <- "101" @@ -55,7 +56,7 @@ test_that("character asIntegerDS - FALSE", { expect_equal(res, 101) }) -context("asIntegerDS::smk::character vector") +# context("asIntegerDS::smk::character vector") test_that("character vector asIntegerDS", { input <- c("101", "202", "303", "404", "505") @@ -74,6 +75,6 @@ test_that("character vector asIntegerDS", { # Done # -context("asIntegerDS::smk::shutdown") +# context("asIntegerDS::smk::shutdown") -context("asIntegerDS::smk::done") +# context("asIntegerDS::smk::done") diff --git a/tests/testthat/test-smk-asListDS.R b/tests/testthat/test-smk-asListDS.R index 7caa9368..5d448109 100644 --- a/tests/testthat/test-smk-asListDS.R +++ b/tests/testthat/test-smk-asListDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("asListDS::smk::setup") +# context("asListDS::smk::setup") # # Tests # -context("asListDS::smk::simple") +# context("asListDS::smk::simple") test_that("simple asListDS", { input <- list(v1 = c(1, 2, 3), v2 = c(4, 5, 6)) newobj.name <- 'newobj' @@ -41,6 +42,6 @@ test_that("simple asListDS", { # Done # -context("asListDS::smk::shutdown") +# context("asListDS::smk::shutdown") -context("asListDS::smk::done") +# context("asListDS::smk::done") diff --git a/tests/testthat/test-smk-asLogicalDS.R b/tests/testthat/test-smk-asLogicalDS.R index d931ad2b..3ea78d6e 100644 --- a/tests/testthat/test-smk-asLogicalDS.R +++ b/tests/testthat/test-smk-asLogicalDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("asLogicalDS::smk::setup") +# context("asLogicalDS::smk::setup") # # Tests # -context("asLogicalDS::smk::integer") +# context("asLogicalDS::smk::integer") test_that("simple asLogicalDS integer - FALSE", { input <- 0L @@ -39,7 +40,7 @@ test_that("simple asLogicalDS integer - TRUE", { expect_equal(res, TRUE) }) -context("asLogicalDS::smk::integer vector") +# context("asLogicalDS::smk::integer vector") test_that("simple asLogicalDS integer vector", { input <- c(1L, 0L, 1L, 0L, 1L) @@ -54,7 +55,7 @@ test_that("simple asLogicalDS integer vector", { expect_equal(res[5], TRUE) }) -context("asLogicalDS::smk::numeric") +# context("asLogicalDS::smk::numeric") test_that("simple asLogicalDS numeric - FALSE", { input <- 0.0 @@ -75,7 +76,7 @@ test_that("simple asLogicalDS numeric - TRUE", { expect_equal(res, TRUE) }) -context("asLogicalDS::smk::numeric vector") +# context("asLogicalDS::smk::numeric vector") test_that("simple asLogicalDS numeric vector", { input <- c(1.0, 0.0, 1.0, 0.0, 1.0) @@ -90,7 +91,7 @@ test_that("simple asLogicalDS numeric vector", { expect_equal(res[5], TRUE) }) -context("asLogicalDS::smk::character") +# context("asLogicalDS::smk::character") test_that("simple asLogicalDS, character - FALSE", { input <- "F" @@ -170,6 +171,6 @@ test_that("simple asLogicalDS, character vector", { # Done # -context("asLogicalDS::smk::shutdown") +# context("asLogicalDS::smk::shutdown") -context("asLogicalDS::smk::done") +# context("asLogicalDS::smk::done") diff --git a/tests/testthat/test-smk-asMatrixDS.R b/tests/testthat/test-smk-asMatrixDS.R index 6d873a5f..71222625 100644 --- a/tests/testthat/test-smk-asMatrixDS.R +++ b/tests/testthat/test-smk-asMatrixDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("asMatrixDS::smk::setup") +# context("asMatrixDS::smk::setup") # # Tests # -context("asMatrixDS::smk::simple") +# context("asMatrixDS::smk::simple") test_that("simple asMatrixDS", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -59,6 +60,6 @@ test_that("simple asMatrixDS", { # Done # -context("asMatrixDS::smk::shutdown") +# context("asMatrixDS::smk::shutdown") -context("asMatrixDS::smk::done") +# context("asMatrixDS::smk::done") diff --git a/tests/testthat/test-smk-asNumericDS.R b/tests/testthat/test-smk-asNumericDS.R index d1e8d57c..c18782b8 100644 --- a/tests/testthat/test-smk-asNumericDS.R +++ b/tests/testthat/test-smk-asNumericDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("asNumericDS::smk::setup") +# context("asNumericDS::smk::setup") # # Tests # -context("asNumericDS::smk::character") +# context("asNumericDS::smk::character") test_that("character asNumericDS - FALSE", { input <- "101" @@ -29,7 +30,7 @@ test_that("character asNumericDS - FALSE", { expect_equal(res, 101) }) -context("asNumericDS::smk::character vector") +# context("asNumericDS::smk::character vector") test_that("character vector asNumericDS", { input <- c("101", "202", "303", "404", "505") @@ -44,7 +45,7 @@ test_that("character vector asNumericDS", { expect_equal(res[5], 505) }) -context("asNumericDS::smk::character 'non numeric' vector") +# context("asNumericDS::smk::character 'non numeric' vector") test_that("character 'non numeric' vector asNumericDS", { input <- c("aa", "bb", "cc", "dd", "ee") @@ -59,7 +60,7 @@ test_that("character 'non numeric' vector asNumericDS", { expect_equal(res[5], 5) }) -context("asNumericDS::smk::factor vector") +# context("asNumericDS::smk::factor vector") test_that("factor vector asNumericDS", { vec <- c("101", "202", "303", "404", "505") input <- as.factor(vec) @@ -75,7 +76,7 @@ test_that("factor vector asNumericDS", { expect_equal(res[5], 505) }) -context("asNumericDS::smk::factor rev vector") +# context("asNumericDS::smk::factor rev vector") test_that("factor vector asNumericDS", { vec <- c("505", "404", "303", "202", "101") input <- as.factor(vec) @@ -91,7 +92,7 @@ test_that("factor vector asNumericDS", { expect_equal(res[5], 101) }) -context("asNumericDS::smk::factor numeric levels vector") +# context("asNumericDS::smk::factor numeric levels vector") test_that("factor numeric levels vector asNumericDS", { vec <- c("aa", "bb", "cc", "dd", "ee") input <- as.factor(vec) @@ -108,7 +109,7 @@ test_that("factor numeric levels vector asNumericDS", { expect_equal(res[5], 55) }) -context("asNumericDS::smk::factor vector with only numbers in its values") +# context("asNumericDS::smk::factor vector with only numbers in its values") test_that("factor vector with only numbers in its values asNumericDS", { input <- as.factor(c('1','1','2','2','1')) @@ -123,7 +124,7 @@ test_that("factor vector with only numbers in its values asNumericDS", { expect_equal(res[5], 1) }) -context("asNumericDS::smk::factor vector with only characters in its values") +# context("asNumericDS::smk::factor vector with only characters in its values") test_that("factor vector with only characters in its values asNumericDS", { input <- as.factor(c('b','b','a','a','b')) @@ -138,7 +139,7 @@ test_that("factor vector with only characters in its values asNumericDS", { expect_equal(res[5], 2) }) -context("asNumericDS::smk::character vector with only numbers in its values") +# context("asNumericDS::smk::character vector with only numbers in its values") test_that("factor vector with only numbers in its values asNumericDS", { input <- c('1','1','2','2','1') @@ -153,7 +154,7 @@ test_that("factor vector with only numbers in its values asNumericDS", { expect_equal(res[5], 1) }) -context("asNumericDS::smk::character vector with only characters in its values") +# context("asNumericDS::smk::character vector with only characters in its values") test_that("character vector with only characters in its values asNumericDS", { input <- c('b','b','a','a','b') @@ -168,7 +169,7 @@ test_that("character vector with only characters in its values asNumericDS", { expect_equal(res[5], 2) }) -context("asNumericDS::smk::character vector with strings having characters and numbers") +# context("asNumericDS::smk::character vector with strings having characters and numbers") test_that("character vector with strings having characters and numbers asNumericDS", { input <- c('b1','b2','1a','a','b') @@ -183,7 +184,7 @@ test_that("character vector with strings having characters and numbers asNumeric expect_equal(res[5], 3) }) -context("asNumericDS::smk::logical vector") +# context("asNumericDS::smk::logical vector") test_that("logical vector asNumericDS", { input <- c(TRUE, TRUE, FALSE, TRUE) @@ -197,7 +198,7 @@ test_that("logical vector asNumericDS", { expect_equal(res[4], 1) }) -context("asNumericDS::smk::logical character vector") +# context("asNumericDS::smk::logical character vector") test_that("logical vector character asNumericDS", { input <- c("TRUE", "TRUE", "FALSE", "TRUE") @@ -211,7 +212,7 @@ test_that("logical vector character asNumericDS", { expect_equal(res[4], 2) }) -context("asNumericDS::smk::integer vector") +# context("asNumericDS::smk::integer vector") test_that("integer vector asNumericDS", { input <- as.integer(c('1','1','2','2','1')) @@ -230,6 +231,6 @@ test_that("integer vector asNumericDS", { # Done # -context("asNumericDS::smk::shutdown") +# context("asNumericDS::smk::shutdown") -context("asNumericDS::smk::done") +# context("asNumericDS::smk::done") diff --git a/tests/testthat/test-smk-aucDS.R b/tests/testthat/test-smk-aucDS.R index 800bbcf4..2e03ccdb 100644 --- a/tests/testthat/test-smk-aucDS.R +++ b/tests/testthat/test-smk-aucDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("aucDS::smk::setup") +# context("aucDS::smk::setup") # # Tests @@ -39,6 +40,6 @@ test_that("aucDS", { # Done # -context("aucDS::smk::shutdown") +# context("aucDS::smk::shutdown") -context("aucDS::smk::done") +# context("aucDS::smk::done") diff --git a/tests/testthat/test-smk-bp_standardsDS.R b/tests/testthat/test-smk-bp_standardsDS.R index 906dd34f..fe8b9bc1 100644 --- a/tests/testthat/test-smk-bp_standardsDS.R +++ b/tests/testthat/test-smk-bp_standardsDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("bp_standardsDS::smk::setup") +# context("bp_standardsDS::smk::setup") # # Tests # -context("bp_standardsDS::smk::systolic") +# context("bp_standardsDS::smk::systolic") test_that("systolic bp_standardsDS", { sex <- c(2, 2, 2, 2, 2, 1, 2, 1, 2, 1) @@ -46,7 +47,7 @@ test_that("systolic bp_standardsDS", { }) -context("bp_standardsDS::smk::diastolic") +# context("bp_standardsDS::smk::diastolic") test_that("diastolic bp_standardsDS", { sex <- c(2, 2, 2, 2, 2, 1, 2, 1, 2, 1) @@ -79,6 +80,6 @@ test_that("diastolic bp_standardsDS", { # Done # -context("bp_standardsDS::smk::shutdown") +# context("bp_standardsDS::smk::shutdown") -context("bp_standardsDS::smk::done") +# context("bp_standardsDS::smk::done") diff --git a/tests/testthat/test-smk-cDS.R b/tests/testthat/test-smk-cDS.R index b3df1a65..0f9842fc 100644 --- a/tests/testthat/test-smk-cDS.R +++ b/tests/testthat/test-smk-cDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("cDS::smk::setup") +# context("cDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("cDS::smk::numeric list") +# context("cDS::smk::numeric list") test_that("numeric list cDS", { input <- list(a=0.0, b=1.0, c=2.0, d=3.0) @@ -34,7 +35,7 @@ test_that("numeric list cDS", { expect_equal(res[[4]], 3.0) }) -context("cDS::smk::character list") +# context("cDS::smk::character list") test_that("character list cDS", { input <- list(a="0.0", b="1.0", c="2.0", d="3.0") @@ -48,7 +49,7 @@ test_that("character list cDS", { expect_equal(res[[4]], "3.0") }) -context("cDS::smk::numeric list small") +# context("cDS::smk::numeric list small") test_that("single numeric list small cDS", { input <- list(a=0, b=1) @@ -60,7 +61,7 @@ test_that("single numeric list small cDS", { expect_equal(res[[2]], NA) }) -context("cDS::smk::empty list") +# context("cDS::smk::empty list") test_that("empty list cDS", { input <- list() @@ -74,6 +75,6 @@ test_that("empty list cDS", { # Done # -context("cDS::smk::shutdown") +# context("cDS::smk::shutdown") -context("cDS::smk::done") +# context("cDS::smk::done") diff --git a/tests/testthat/test-smk-cbindDS.R b/tests/testthat/test-smk-cbindDS.R index c1ed0a2f..11fe1ef3 100644 --- a/tests/testthat/test-smk-cbindDS.R +++ b/tests/testthat/test-smk-cbindDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("cbindDS::smk::setup") +# context("cbindDS::smk::setup") # # Tests # -context("cbindDS::smk::simple") +# context("cbindDS::smk::simple") test_that("simple cbindDS", { inputs <- 'input1,input2' input1 <- c(0.0, 1.0, 2.0, 3.0) @@ -44,6 +45,6 @@ test_that("simple cbindDS", { # Done # -context("cbindDS::smk::shutdown") +# context("cbindDS::smk::shutdown") -context("cbindDS::smk::done") +# context("cbindDS::smk::done") diff --git a/tests/testthat/test-smk-changeRefGroupDS.R b/tests/testthat/test-smk-changeRefGroupDS.R index 0bdd87ae..3d94fde7 100644 --- a/tests/testthat/test-smk-changeRefGroupDS.R +++ b/tests/testthat/test-smk-changeRefGroupDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("changeRefGroupDS::smk::setup") +# context("changeRefGroupDS::smk::setup") # # Tests # -context("changeRefGroupDS::smk") +# context("changeRefGroupDS::smk") test_that("simple changeRefGroupDS, reorderByRef is FALSE", { x <- c(8, 1, 6, 1, 4, 1, 2, 1) xf <- as.factor(x) @@ -107,6 +108,6 @@ test_that("simple changeRefGroupDS, reorderByRef is TRUE", { # Done # -context("changeRefGroupDS::smk::shutdown") +# context("changeRefGroupDS::smk::shutdown") -context("changeRefGroupDS::smk::done") +# context("changeRefGroupDS::smk::done") diff --git a/tests/testthat/test-smk-checkNegValueDS.R b/tests/testthat/test-smk-checkNegValueDS.R index 52b64cce..487a9709 100644 --- a/tests/testthat/test-smk-checkNegValueDS.R +++ b/tests/testthat/test-smk-checkNegValueDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("checkNegValueDS::smk::setup") +# context("checkNegValueDS::smk::setup") # # Tests # -context("checkNegValueDS::smk::with no neg") +# context("checkNegValueDS::smk::with no neg") test_that("simple checkNegValueDS, with no neg and no NA", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -39,7 +40,7 @@ test_that("simple checkNegValueDS, with no neg and NA", { expect_equal(res, FALSE) }) -context("checkNegValueDS::smk::with neg") +# context("checkNegValueDS::smk::with neg") test_that("simple checkNegValueDS, with neg and no NA", { input <- c(0.0, -1.0, -2.0, 3.0, -4.0, 5.0, -6.0, 7.0) @@ -64,6 +65,6 @@ test_that("simple checkNegValueDS, with neg and NA", { # Done # -context("checkNegValueDS::smk::shutdown") +# context("checkNegValueDS::smk::shutdown") -context("checkNegValueDS::smk::done") +# context("checkNegValueDS::smk::done") diff --git a/tests/testthat/test-smk-classDS.R b/tests/testthat/test-smk-classDS.R index 4b3d71b3..d2efcf40 100644 --- a/tests/testthat/test-smk-classDS.R +++ b/tests/testthat/test-smk-classDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("classDS::smk::setup") +# context("classDS::smk::setup") # # Tests # -context("classDS::smk::character") +# context("classDS::smk::character") test_that("simple classDS, character", { input <- "value" @@ -39,7 +40,7 @@ test_that("simple classDS, character vector", { expect_equal(res, "character") }) -context("classDS::smk::integer") +# context("classDS::smk::integer") test_that("simple classDS, integer", { input <- 1L @@ -60,7 +61,7 @@ test_that("simple classDS, integer vector", { expect_equal(res, "integer") }) -context("classDS::smk::numeric") +# context("classDS::smk::numeric") test_that("simple classDS, numeric", { input <- 1.1 @@ -81,7 +82,7 @@ test_that("simple classDS, numeric vector", { expect_equal(res, "numeric") }) -context("classDS::smk::logical") +# context("classDS::smk::logical") test_that("simple classDS, logical, FALSE", { input <- FALSE @@ -112,7 +113,7 @@ test_that("simple classDS, logical vector", { expect_equal(res, "logical") }) -context("classDS::smk::data.frame") +# context("classDS::smk::data.frame") test_that("simple classDS, data.frame", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -123,7 +124,7 @@ test_that("simple classDS, data.frame", { expect_equal(res, "data.frame") }) -context("classDS::smk::array") +# context("classDS::smk::array") test_that("simple classDS, array", { input <- array(c(0.0, 1.0, 2.0, 3.0, 4.0)) @@ -134,7 +135,7 @@ test_that("simple classDS, array", { expect_equal(res, "array") }) -context("classDS::smk::matrix") +# context("classDS::smk::matrix") test_that("simple classDS, matrix", { input <- matrix(c(0.0, 1.0, 2.0, 3.0, 4.0)) @@ -154,7 +155,7 @@ test_that("simple classDS, matrix", { } }) -context("classDS::smk::data.matrix") +# context("classDS::smk::data.matrix") test_that("simple classDS, data.matrix", { input <- data.matrix(data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0))) @@ -174,7 +175,7 @@ test_that("simple classDS, data.matrix", { } }) -context("classDS::smk::date") +# context("classDS::smk::date") test_that("simple classDS, date", { input <- Sys.Date() @@ -185,7 +186,7 @@ test_that("simple classDS, date", { expect_equal(res, "Date") }) -context("classDS::smk::formula") +# context("classDS::smk::formula") test_that("simple classDS, formula", { input <- X ~ A + B @@ -196,7 +197,7 @@ test_that("simple classDS, formula", { expect_equal(res, "formula") }) -context("classDS::smk::environment") +# context("classDS::smk::environment") test_that("simple classDS, environment", { input <- environment() @@ -207,7 +208,7 @@ test_that("simple classDS, environment", { expect_equal(res, "environment") }) -context("classDS::smk::NA") +# context("classDS::smk::NA") test_that("special classDS, NA", { input <- NA @@ -218,7 +219,7 @@ test_that("special classDS, NA", { expect_equal(res, "logical") }) -context("classDS::smk::NULL") +# context("classDS::smk::NULL") test_that("special classDS, NULL", { input <- NULL @@ -233,6 +234,6 @@ test_that("special classDS, NULL", { # Done # -context("classDS::smk::shutdown") +# context("classDS::smk::shutdown") -context("classDS::smk::done") +# context("classDS::smk::done") diff --git a/tests/testthat/test-smk-colnamesDS.R b/tests/testthat/test-smk-colnamesDS.R index 2c4d3e3c..af29ac42 100644 --- a/tests/testthat/test-smk-colnamesDS.R +++ b/tests/testthat/test-smk-colnamesDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("colnamesDS::smk::setup") +# context("colnamesDS::smk::setup") # # Tests # -context("colnamesDS::smk::data.frame") +# context("colnamesDS::smk::data.frame") test_that("simple colnamesDS, data.frame", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -30,7 +31,7 @@ test_that("simple colnamesDS, data.frame", { expect_true("v2" %in% res) }) -context("colnamesDS::smk::data.matrix") +# context("colnamesDS::smk::data.matrix") test_that("simple colnamesDS, data.matrix", { input <- data.matrix(data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0))) @@ -46,6 +47,6 @@ test_that("simple colnamesDS, data.matrix", { # Done # -context("colnamesDS::smk::shutdown") +# context("colnamesDS::smk::shutdown") -context("colnamesDS::smk::done") +# context("colnamesDS::smk::done") diff --git a/tests/testthat/test-smk-completeCasesDS.R b/tests/testthat/test-smk-completeCasesDS.R index 68bedebf..2ba7b913 100644 --- a/tests/testthat/test-smk-completeCasesDS.R +++ b/tests/testthat/test-smk-completeCasesDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("completeCasesDS::smk::setup") +# context("completeCasesDS::smk::setup") # # Tests # -context("completeCasesDS::smk::vector") +# context("completeCasesDS::smk::vector") test_that("simple completeCasesDS, vector, with no NAs", { input <- c(1.1, 2.1, 3.1, 4.1) @@ -44,7 +45,7 @@ test_that("simple completeCasesDS, vector, with NAs", { expect_equal(res[3], 4.1) }) -context("completeCasesDS::smk::data.frame") +# context("completeCasesDS::smk::data.frame") test_that("simple completeCasesDS, data.frame, with no NAs", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -93,7 +94,7 @@ test_that("simple completeCasesDS, data.frame, with NAs", { expect_equal(res.colnames[2], "v2") }) -context("completeCasesDS::smk::matrix") +# context("completeCasesDS::smk::matrix") test_that("simple completeCasesDS, matrix, with no NAs", { input <- matrix(c(0.0, 1.0, 2.0, 3.0, 4.0)) @@ -120,7 +121,7 @@ test_that("simple completeCasesDS, matrix, with NAs", { expect_equal(res[3], 4.0) }) -context("completeCasesDS::smk::data.matrix") +# context("completeCasesDS::smk::data.matrix") test_that("simple completeCasesDS, data.matrix, with no NAs", { input <- data.matrix(data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0))) @@ -193,6 +194,6 @@ test_that("simple completeCasesDS, data.matrix, with NAs", { # Done # -context("completeCasesDS::smk::shutdown") +# context("completeCasesDS::smk::shutdown") -context("completeCasesDS::smk::done") +# context("completeCasesDS::smk::done") diff --git a/tests/testthat/test-smk-corDS.R b/tests/testthat/test-smk-corDS.R index c0c4c06e..bdc3607c 100644 --- a/tests/testthat/test-smk-corDS.R +++ b/tests/testthat/test-smk-corDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("corDS::smk::setup") +# context("corDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -#context("corDS::smk::pairwise without na") +# context("corDS::smk::pairwise without na") #test_that("simple corDS, pairwise, full", { # x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) # y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -280,7 +281,7 @@ set.standard.disclosure.settings() # expect_equal(res$sums.of.squares[4], 141.06) #}) -#context("corDS::smk::pairwise with na") +# context("corDS::smk::pairwise with na") #test_that("simple corDS, pairwise, some", { # x <- c(0.0, NA, 2.0, 3.0, NA, 5.0, NA, 7.0) # y <- c(0.0, 1.0, NA, 3.0, 4.0, NA, NA, 7.0) @@ -367,7 +368,7 @@ set.standard.disclosure.settings() # expect_equal(res$sums.of.squares[4], 75.0) #}) -context("corDS::smk::casewise without na") +# context("corDS::smk::casewise without na") test_that("simple corDS, casewise, full", { x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -629,7 +630,7 @@ test_that("simple corDS, casewise, some", { expect_equal(res$sums.of.squares[4], 141.06) }) -context("corDS::smk::casewise with na") +# context("corDS::smk::casewise with na") test_that("simple corDS, casewise, some", { x <- c(0.0, NA, 2.0, 3.0, NA, 5.0, NA, 7.0) y <- c(0.0, 1.0, NA, 3.0, 4.0, NA, NA, 7.0) @@ -721,6 +722,6 @@ test_that("simple corDS, casewise, some", { # Done # -context("corDS::smk::shutdown") +# context("corDS::smk::shutdown") -context("corDS::smk::done") +# context("corDS::smk::done") diff --git a/tests/testthat/test-smk-corTestDS.R b/tests/testthat/test-smk-corTestDS.R index a36e2082..1314b933 100644 --- a/tests/testthat/test-smk-corTestDS.R +++ b/tests/testthat/test-smk-corTestDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("corTestDS::smk::setup") +# context("corTestDS::smk::setup") # # Tests @@ -20,7 +21,7 @@ context("corTestDS::smk::setup") ########### -context("corTestDS::smk::without na, pearson") +# context("corTestDS::smk::without na, pearson") test_that("simple corTestDS, full, without na, pearson", { x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -180,7 +181,7 @@ test_that("simple corTestDS, some, pearson, without na, pearson", { expect_equal(res$`Correlation test`$conf.int[[2]], 0.9998169, tolerance = 1e-6) }) -context("corTestDS::smk::with na, pearson") +# context("corTestDS::smk::with na, pearson") test_that("simple corTestDS, some, with na, pearson", { x <- c(NA, 1.0, 2.0, 3.0, NA, 5.0, NA, 7.0) y <- c(0.0, 1.0, NA, 3.0, 4.0, NA, NA, 7.0) @@ -229,7 +230,7 @@ test_that("simple corTestDS, some, with na, pearson", { expect_equal(res$`Correlation test`$data.name[[1]], "x.var and y.var") }) -context("corTestDS::smk::without na, kendall") +# context("corTestDS::smk::without na, kendall") test_that("simple corTestDS, full, without na, kendall", { x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -368,7 +369,7 @@ test_that("simple corTestDS, some, kendall, without na, kendall", { expect_equal(res$`Correlation test`$data.name[[1]], "x.var and y.var") }) -context("corTestDS::smk::with na, kendall") +# context("corTestDS::smk::with na, kendall") test_that("simple corTestDS, some, with na, kendall", { x <- c(0.0, NA, 2.0, 3.0, NA, 5.0, NA, 7.0) y <- c(0.0, 1.0, NA, 3.0, 4.0, NA, NA, 7.0) @@ -415,7 +416,7 @@ test_that("simple corTestDS, some, with na, kendall", { expect_equal(res$`Correlation test`$data.name[[1]], "x.var and y.var") }) -context("corTestDS::smk::without na, spearman") +# context("corTestDS::smk::without na, spearman") test_that("simple corTestDS, full, without na, spearman", { x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -554,7 +555,7 @@ test_that("simple corTestDS, some, spearman, without na, spearman", { expect_equal(res$`Correlation test`$data.name[[1]], "x.var and y.var") }) -context("corTestDS::smk::with na, spearman") +# context("corTestDS::smk::with na, spearman") test_that("simple corTestDS, some, with na, spearman", { x <- c(0.0, NA, 2.0, 3.0, NA, 5.0, NA, 7.0) y <- c(0.0, 1.0, NA, 3.0, 4.0, NA, NA, 7.0) @@ -605,7 +606,7 @@ test_that("simple corTestDS, some, with na, spearman", { # Done # -context("corTestDS::smk::shutdown") +# context("corTestDS::smk::shutdown") -context("corTestDS::smk::done") +# context("corTestDS::smk::done") diff --git a/tests/testthat/test-smk-covDS.R b/tests/testthat/test-smk-covDS.R index da05102c..ce731938 100644 --- a/tests/testthat/test-smk-covDS.R +++ b/tests/testthat/test-smk-covDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("covDS::smk::setup") +# context("covDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("covDS::smk::casewise.complete") +# context("covDS::smk::casewise.complete") test_that("numeric covDS, casewise.complete", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0), v2 = c(7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0)) @@ -123,7 +124,7 @@ test_that("numeric covDS, casewise.complete", { expect_true(is.na(res$errorMessage)) }) -context("covDS::smk::pairwise.complete") +# context("covDS::smk::pairwise.complete") test_that("numeric covDS, pairwise.complete", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0), v2 = c(7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0)) @@ -235,6 +236,6 @@ test_that("numeric covDS, pairwise.complete", { # Done # -context("covDS::smk::shutdown") +# context("covDS::smk::shutdown") -context("covDS::smk::done") +# context("covDS::smk::done") diff --git a/tests/testthat/test-smk-dataFrameDS.R b/tests/testthat/test-smk-dataFrameDS.R index af6ff6d5..18fc3b4b 100644 --- a/tests/testthat/test-smk-dataFrameDS.R +++ b/tests/testthat/test-smk-dataFrameDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("dataFrameDS::smk::setup") +# context("dataFrameDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("dataFrameDS::smk") +# 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) @@ -81,10 +82,10 @@ test_that("simple dataFrameDS, strAsFactors is TRUE", { # Stutdown # -context("dataFrameDS::smk::shutdown") +# context("dataFrameDS::smk::shutdown") # # Done # -context("dataFrameDS::smk::done") +# context("dataFrameDS::smk::done") diff --git a/tests/testthat/test-smk-dataFrameFillDS.R b/tests/testthat/test-smk-dataFrameFillDS.R index 5cc880f7..8da7a882 100644 --- a/tests/testthat/test-smk-dataFrameFillDS.R +++ b/tests/testthat/test-smk-dataFrameFillDS.R @@ -1,6 +1,6 @@ - #------------------------------------------------------------------------------- # 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. @@ -13,13 +13,13 @@ # Set up # -context("dataFrameFillDS::smk::setup") +# context("dataFrameFillDS::smk::setup") # # Tests # -context("dataFrameFillDS::smk") +# context("dataFrameFillDS::smk") test_that("simple dataFrameFillDS, ascending, numeric", { df <- data.frame(v1 = c(-2.0, -3.0, 4.0, 2.0, 1.0, 0.0, -1.0, 3.0), v2 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0)) allNames.transmit <- "v1,v2,v3,v4,v5,v6,v7" @@ -94,10 +94,10 @@ test_that("simple dataFrameFillDS, ascending, numeric", { # Shutdown # -context("dataFrameFillDS::smk::shutdown") +# context("dataFrameFillDS::smk::shutdown") # # Done # -context("dataFrameFillDS::smk::done") +# context("dataFrameFillDS::smk::done") diff --git a/tests/testthat/test-smk-dataFrameSortDS.R b/tests/testthat/test-smk-dataFrameSortDS.R index b81965e0..39a7378b 100644 --- a/tests/testthat/test-smk-dataFrameSortDS.R +++ b/tests/testthat/test-smk-dataFrameSortDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("dataFrameSortDS::smk::setup") +# context("dataFrameSortDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("dataFrameSortDS::smk::numeric input") +# context("dataFrameSortDS::smk::numeric input") test_that("simple dataFrameSortDS, ascending, default", { df <- data.frame(v1 = c(-2.0, -3.0, 4.0, 2.0, 1.0, 0.0, -1.0, 3.0), v2 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0)) sort.key.name <- "df$v1" @@ -243,7 +244,7 @@ test_that("simple dataFrameSortDS, descending, alphabetic", { expect_equal(res$v2[8], 6.0) }) -context("dataFrameSortDS::smk::string input") +# context("dataFrameSortDS::smk::string input") test_that("simple dataFrameSortDS, ascending, default", { df <- data.frame(v1 = c("-2.0", "-3.0", "4.0", "2.0", "1.0", "0.0", "-1.0", "3.0"), v2 = c("0.0", "1.0", "2.0", "3.0", "4.0", "5.0", "6.0", "7.0"), stringsAsFactors = FALSE) sort.key.name <- "df$v1" @@ -471,6 +472,6 @@ test_that("simple dataFrameSortDS, descending, alphabetic", { # Done # -context("dataFrameSortDS::smk::shutdown") +# context("dataFrameSortDS::smk::shutdown") -context("dataFrameSortDS::smk::done") +# context("dataFrameSortDS::smk::done") diff --git a/tests/testthat/test-smk-dataFrameSubsetDS1.R b/tests/testthat/test-smk-dataFrameSubsetDS1.R index 93dbca26..c519cefa 100644 --- a/tests/testthat/test-smk-dataFrameSubsetDS1.R +++ b/tests/testthat/test-smk-dataFrameSubsetDS1.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("gamlssDS::smk::setup") +# context("gamlssDS::smk::setup") set.standard.disclosure.settings() @@ -21,7 +22,7 @@ set.standard.disclosure.settings() # Tests # -context("dataFrameSubsetDS1::smk::test1") +# context("dataFrameSubsetDS1::smk::test1") test_that("test1 dataFrameSubsetDS1", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) @@ -42,7 +43,7 @@ test_that("test1 dataFrameSubsetDS1", { }) -context("dataFrameSubsetDS1::smk::test2") +# context("dataFrameSubsetDS1::smk::test2") test_that("test2 dataFrameSubsetDS1", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) @@ -77,6 +78,6 @@ test_that("test2 dataFrameSubsetDS1", { # Done # -context("dataFrameSubsetDS1::smk::shutdown") +# context("dataFrameSubsetDS1::smk::shutdown") -context("dataFrameSubsetDS1::smk::done") +# context("dataFrameSubsetDS1::smk::done") diff --git a/tests/testthat/test-smk-dataFrameSubsetDS2.R b/tests/testthat/test-smk-dataFrameSubsetDS2.R index 619da16c..c93dc595 100644 --- a/tests/testthat/test-smk-dataFrameSubsetDS2.R +++ b/tests/testthat/test-smk-dataFrameSubsetDS2.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("gamlssDS::smk::setup") +# contect("gamlssDS::smk::setup") set.standard.disclosure.settings() @@ -21,7 +22,7 @@ set.standard.disclosure.settings() # Tests # -context("dataFrameSubsetDS2::smk::test1") +# contect("dataFrameSubsetDS2::smk::test1") test_that("test1 dataFrameSubsetDS2", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) @@ -47,7 +48,7 @@ test_that("test1 dataFrameSubsetDS2", { }) -context("dataFrameSubsetDS2::smk::test2") +# contect("dataFrameSubsetDS2::smk::test2") test_that("test2 dataFrameSubsetDS2", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) @@ -74,6 +75,6 @@ test_that("test2 dataFrameSubsetDS2", { # Done # -context("dataFrameSubsetDS2::smk::shutdown") +# contect("dataFrameSubsetDS2::smk::shutdown") -context("dataFrameSubsetDS2::smk::done") +# contect("dataFrameSubsetDS2::smk::done") diff --git a/tests/testthat/test-smk-densityGridDS.R b/tests/testthat/test-smk-densityGridDS.R index 612386bb..2c075a4b 100644 --- a/tests/testthat/test-smk-densityGridDS.R +++ b/tests/testthat/test-smk-densityGridDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("densityGridDS::smk::setup") +# context("densityGridDS::smk::setup") set.standard.disclosure.settings() @@ -21,7 +22,7 @@ set.standard.disclosure.settings() # Tests # -context("densityGridDS::smk") +# context("densityGridDS::smk") test_that("densityGridDS", { xvect <- c(11.95, 10.06, 9.98, 9.50, 12.26, 9.66, 11.08, 12.29, 11.00, 9.91, @@ -53,6 +54,6 @@ test_that("densityGridDS", { # Done # -context("densityGridDS::smk::shutdown") +# context("densityGridDS::smk::shutdown") -context("densityGridDS::smk::done") +# context("densityGridDS::smk::done") diff --git a/tests/testthat/test-smk-dimDS.R b/tests/testthat/test-smk-dimDS.R index 5dbdb6de..7915e9a1 100644 --- a/tests/testthat/test-smk-dimDS.R +++ b/tests/testthat/test-smk-dimDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("dimDS::smk::setup") +# context("dimDS::smk::setup") # # Tests # -context("dimDS::smk::numeric") +# context("dimDS::smk::numeric") test_that("numeric dimDS", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -30,7 +31,7 @@ test_that("numeric dimDS", { expect_equal(res[2], 2) }) -context("dimDS::smk::character") +# context("dimDS::smk::character") test_that("character dimDS", { input <- data.frame(v1 = c("0.0", "1.0", "2.0", "3.0", "4.0"), v2 = c("4.0", "3.0", "2.0", "1.0", "0.0"), stringsAsFactors = FALSE) @@ -46,6 +47,6 @@ test_that("character dimDS", { # Done # -context("dimDS::smk::shutdown") +# context("dimDS::smk::shutdown") -context("dimDS::smk::done") +# context("dimDS::smk::done") diff --git a/tests/testthat/test-smk-extract.R b/tests/testthat/test-smk-extract.R index bd471a67..9b1af851 100644 --- a/tests/testthat/test-smk-extract.R +++ b/tests/testthat/test-smk-extract.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("extract::smk::setup") +# context("extract::smk::setup") # # Tests # -context("extract::smk::simple") +# context("extract::smk::simple") test_that("simple extract no holder", { input <- "variable" @@ -45,7 +46,7 @@ test_that("simple extract", { expect_equal(res$elements, "variable") }) -context("extract::smk::simple vector") +# context("extract::smk::simple vector") test_that("simple extract no holder, vector", { input <- c("v1", "v2", "v3", "v4") @@ -107,6 +108,6 @@ test_that("simple extract, mixed, vector", { # Done # -context("extract::smk::shutdown") +# context("extract::smk::shutdown") -context("extract::smk::done") +# context("extract::smk::done") diff --git a/tests/testthat/test-smk-gamlssDS.R b/tests/testthat/test-smk-gamlssDS.R index 636e0f26..de284148 100644 --- a/tests/testthat/test-smk-gamlssDS.R +++ b/tests/testthat/test-smk-gamlssDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("gamlssDS::smk::setup") +# context("gamlssDS::smk::setup") set.standard.disclosure.settings() @@ -21,7 +22,7 @@ set.standard.disclosure.settings() # Tests # -context("gamlssDS::smk::birthweight") +# context("gamlssDS::smk::birthweight") test_that("birthweight gamlssDS", { D <- as.data.frame(matrix(NA, nrow=20, ncol=2)) @@ -88,6 +89,6 @@ test_that("birthweight gamlssDS", { # Done # -context("gamlssDS::smk::shutdown") +# context("gamlssDS::smk::shutdown") -context("gamlssDS::smk::done") +# context("gamlssDS::smk::done") diff --git a/tests/testthat/test-smk-getWGSRDS.R b/tests/testthat/test-smk-getWGSRDS.R index 0036fcdf..73d0eda1 100644 --- a/tests/testthat/test-smk-getWGSRDS.R +++ b/tests/testthat/test-smk-getWGSRDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("getWGSRDS::smk::setup") +# context("getWGSRDS::smk::setup") # # Tests # -context("getWGSRDS::smk::simple") +# context("getWGSRDS::smk::simple") data <- data.frame( age = c(6.0, 42.0, 23.0, 18.0, 52.0, 36.0, 30.0, NA, 29.0, 54.0), @@ -152,6 +153,6 @@ test_that("simple getWGSRDS - mfa", { # Done # -context("getWGSRDS::smk::shutdown") +# context("getWGSRDS::smk::shutdown") -context("getWGSRDS::smk::done") +# context("getWGSRDS::smk::done") diff --git a/tests/testthat/test-smk-hetcorDS.R b/tests/testthat/test-smk-hetcorDS.R index f78d14cc..fd5ca14e 100644 --- a/tests/testthat/test-smk-hetcorDS.R +++ b/tests/testthat/test-smk-hetcorDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("hetcorDS::smk::setup") +# context("hetcorDS::smk::setup") set.standard.disclosure.settings() @@ -21,7 +22,7 @@ set.standard.disclosure.settings() # Tests # -context("hetcorDS::smk") +# context("hetcorDS::smk") test_that("hetcorDS", { D <- as.data.frame(matrix(NA, nrow=20, ncol=3)) @@ -86,6 +87,6 @@ test_that("hetcorDS", { # Done # -context("hetcorDS::smk::shutdown") +# context("hetcorDS::smk::shutdown") -context("hetcorDS::smk::done") \ No newline at end of file +# context("hetcorDS::smk::done") diff --git a/tests/testthat/test-smk-igb_standardsDS.R b/tests/testthat/test-smk-igb_standardsDS.R index 114c88d9..bd3a8f79 100644 --- a/tests/testthat/test-smk-igb_standardsDS.R +++ b/tests/testthat/test-smk-igb_standardsDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("igb_standardsDS::smk::setup") +# context("igb_standardsDS::smk::setup") # # Tests # -context("igb_standardsDS::smk::simple") +# context("igb_standardsDS::smk::simple") data <- data.frame( gagebrth = c(287, 287, 287, 280, 280, 280, 280, 266, 266, 259, @@ -157,6 +158,6 @@ test_that("igb_standardsDS - igb_centile2value", { # Done # -context("igb_standardsDS::smk::shutdown") +# context("igb_standardsDS::smk::shutdown") -context("igb_standardsDS::smk::done") +# context("igb_standardsDS::smk::done") diff --git a/tests/testthat/test-smk-isNaDS.R b/tests/testthat/test-smk-isNaDS.R index e5922d27..766d513c 100644 --- a/tests/testthat/test-smk-isNaDS.R +++ b/tests/testthat/test-smk-isNaDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("isNaDS::smk::setup") +# context("isNaDS::smk::setup") # # Tests # -context("isNaDS::smk::numeric vector") +# context("isNaDS::smk::numeric vector") test_that("numeric vector isNaDS", { input <- c(0.1, 1.1, 2.1, 3.1, 4.1) @@ -49,7 +50,7 @@ test_that("numeric vector isNaDS - with NA all", { expect_equal(res, TRUE) }) -context("isNaDS::smk::character vector") +# context("isNaDS::smk::character vector") test_that("character vector isNaDS", { input <- c("101", "202", "303", "404", "505") @@ -84,6 +85,6 @@ test_that("character vector isNaDS - with NA all", { # Done # -context("isNaDS::smk::shutdown") +# context("isNaDS::smk::shutdown") -context("isNaDS::smk::done") +# context("isNaDS::smk::done") diff --git a/tests/testthat/test-smk-isValidDS.R b/tests/testthat/test-smk-isValidDS.R index c2d3af51..81fc5ade 100644 --- a/tests/testthat/test-smk-isValidDS.R +++ b/tests/testthat/test-smk-isValidDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("isValidDS::smk::setup") +# context("isValidDS::smk::setup") # # Tests # -context("isValidDS::smk::character") +# context("isValidDS::smk::character") test_that("simple isValidDS, character", { input <- "value" @@ -39,7 +40,7 @@ test_that("simple isValidDS, character vector", { expect_equal(res, TRUE) }) -context("isValidDS::smk::integer") +# context("isValidDS::smk::integer") test_that("simple isValidDS, integer", { input <- 1L @@ -60,7 +61,7 @@ test_that("simple isValidDS, integer vector", { expect_equal(res, TRUE) }) -context("isValidDS::smk::numeric") +# context("isValidDS::smk::numeric") test_that("simple isValidDS, numeric", { input <- 1.1 @@ -81,7 +82,7 @@ test_that("simple isValidDS, numeric vector", { expect_equal(res, TRUE) }) -context("isValidDS::smk::logical") +# context("isValidDS::smk::logical") test_that("simple isValidDS, logical, FALSE", { input <- FALSE @@ -142,7 +143,7 @@ test_that("simple isValidDS, factor vector", { expect_equal(res, FALSE) }) -context("isValidDS::smk::data.frame") +# context("isValidDS::smk::data.frame") test_that("simple isValidDS, data.frame", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -153,7 +154,7 @@ test_that("simple isValidDS, data.frame", { expect_equal(res, TRUE) }) -context("isValidDS::smk::array") +# context("isValidDS::smk::array") test_that("simple isValidDS, array", { input <- array(c(0.0, 1.0, 2.0, 3.0, 4.0)) @@ -164,7 +165,7 @@ test_that("simple isValidDS, array", { expect_equal(res, FALSE) }) -context("isValidDS::smk::matrix") +# context("isValidDS::smk::matrix") test_that("simple isValidDS, matrix", { input <- matrix(c(0.0, 1.0, 2.0, 3.0, 4.0)) @@ -175,7 +176,7 @@ test_that("simple isValidDS, matrix", { expect_equal(res, TRUE) }) -context("isValidDS::smk::data.matrix") +# context("isValidDS::smk::data.matrix") test_that("simple isValidDS, data.matrix", { input <- data.matrix(data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0))) @@ -186,7 +187,7 @@ test_that("simple isValidDS, data.matrix", { expect_equal(res, TRUE) }) -context("isValidDS::smk::date") +# context("isValidDS::smk::date") test_that("simple isValidDS, date", { input <- Sys.Date() @@ -197,7 +198,7 @@ test_that("simple isValidDS, date", { expect_equal(res, FALSE) }) -context("isValidDS::smk::formula") +# context("isValidDS::smk::formula") test_that("simple isValidDS, formula", { input <- X ~ A + B @@ -208,7 +209,7 @@ test_that("simple isValidDS, formula", { expect_equal(res, FALSE) }) -context("isValidDS::smk::environment") +# context("isValidDS::smk::environment") test_that("simple isValidDS, environment", { input <- environment() @@ -219,7 +220,7 @@ test_that("simple isValidDS, environment", { expect_equal(res, FALSE) }) -context("isValidDS::smk::NA") +# context("isValidDS::smk::NA") test_that("special isValidDS, NA", { input <- NA @@ -230,7 +231,7 @@ test_that("special isValidDS, NA", { expect_equal(res, FALSE) }) -context("isValidDS::smk::NULL") +# context("isValidDS::smk::NULL") test_that("special isValidDS, NULL", { input <- NULL @@ -245,6 +246,6 @@ test_that("special isValidDS, NULL", { # Done # -context("isValidDS::smk::shutdown") +# context("isValidDS::smk::shutdown") -context("isValidDS::smk::done") +# context("isValidDS::smk::done") diff --git a/tests/testthat/test-smk-kurtosisDS1.R b/tests/testthat/test-smk-kurtosisDS1.R index 62f10307..fe939107 100644 --- a/tests/testthat/test-smk-kurtosisDS1.R +++ b/tests/testthat/test-smk-kurtosisDS1.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("kurtosisDS1::smk::setup") +# context("kurtosisDS1::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("kurtosisDS1::smk::method 1") +# context("kurtosisDS1::smk::method 1") test_that("simple kurtosisDS1, method 1", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) @@ -36,7 +37,7 @@ test_that("simple kurtosisDS1, method 1", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("kurtosisDS1::smk::method 2") +# context("kurtosisDS1::smk::method 2") test_that("simple kurtosisDS1, method 2", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) @@ -52,7 +53,7 @@ test_that("simple kurtosisDS1, method 2", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("kurtosisDS1::smk::method 3") +# context("kurtosisDS1::smk::method 3") test_that("simple kurtosisDS1, method 3", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) @@ -72,6 +73,6 @@ test_that("simple kurtosisDS1, method 3", { # Done # -context("kurtosisDS1::smk::shutdown") +# context("kurtosisDS1::smk::shutdown") -context("kurtosisDS1::smk::done") +# context("kurtosisDS1::smk::done") diff --git a/tests/testthat/test-smk-kurtosisDS2.R b/tests/testthat/test-smk-kurtosisDS2.R index 24833388..8f122a6e 100644 --- a/tests/testthat/test-smk-kurtosisDS2.R +++ b/tests/testthat/test-smk-kurtosisDS2.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("kurtosisDS2::smk::setup") +# context("kurtosisDS2::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("kurtosisDS2::smk") +# context("kurtosisDS2::smk") test_that("simple kurtosisDS2", { input <- c(1.0, 2.0, 2.0, 3.0, 3.0) global.mean <- 2.5 @@ -43,6 +44,6 @@ test_that("simple kurtosisDS2", { # Done # -context("kurtosisDS2::smk::shutdown") +# context("kurtosisDS2::smk::shutdown") -context("kurtosisDS2::smk::done") +# context("kurtosisDS2::smk::done") diff --git a/tests/testthat/test-smk-lengthDS.R b/tests/testthat/test-smk-lengthDS.R index d7cd2bda..b5fad0e7 100644 --- a/tests/testthat/test-smk-lengthDS.R +++ b/tests/testthat/test-smk-lengthDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("lengthDS::smk::setup") +# context("lengthDS::smk::setup") # # Tests # -context("lengthDS::smk::data.frame") +# context("lengthDS::smk::data.frame") test_that("simple lengthDS, numeric data.frame", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -37,7 +38,7 @@ test_that("simple lengthDS, character data.frame", { expect_equal(res, 2) }) -context("lengthDS::smk::vector") +# context("lengthDS::smk::vector") test_that("simple lengthDS, numeric vector", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) @@ -60,6 +61,6 @@ test_that("simple lengthDS, character vector", { # Done # -context("lengthDS::smk::shutdown") +# context("lengthDS::smk::shutdown") -context("lengthDS::smk::done") +# context("lengthDS::smk::done") diff --git a/tests/testthat/test-smk-levelsDS.R b/tests/testthat/test-smk-levelsDS.R index e1b93daa..5ba10980 100644 --- a/tests/testthat/test-smk-levelsDS.R +++ b/tests/testthat/test-smk-levelsDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("levelsDS::smk::setup") +# context("levelsDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("levelsDS::smk::numeric vector") +# context("levelsDS::smk::numeric vector") test_that("numeric vector levelsDS", { input <- as.factor(c(0, 1, 2, 1, 2, 3, 1, 2, 1, 0, 1, 2, 0)) @@ -42,6 +43,6 @@ test_that("numeric vector levelsDS", { # Done # -context("levelsDS::smk::shutdown") +# context("levelsDS::smk::shutdown") -context("levelsDS::smk::done") +# context("levelsDS::smk::done") diff --git a/tests/testthat/test-smk-listDS.R b/tests/testthat/test-smk-listDS.R index f1e12e94..dfd0a171 100644 --- a/tests/testthat/test-smk-listDS.R +++ b/tests/testthat/test-smk-listDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("listDS::smk::setup") +# context("listDS::smk::setup") # # Tests # -context("listDS::smk::simple") +# context("listDS::smk::simple") test_that("simple listDS", { input <- list(v1 = c(1, 2, 3), v2 = c(4, 5, 6)) eltnames <- c('n1', 'n2') @@ -42,6 +43,6 @@ test_that("simple listDS", { # Done # -context("listDS::smk::shutdown") +# context("listDS::smk::shutdown") -context("listDS::smk::done") +# context("listDS::smk::done") diff --git a/tests/testthat/test-smk-listDisclosureSettingsDS.R b/tests/testthat/test-smk-listDisclosureSettingsDS.R index 4ee63cf0..b680b3b3 100644 --- a/tests/testthat/test-smk-listDisclosureSettingsDS.R +++ b/tests/testthat/test-smk-listDisclosureSettingsDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("listDisclosureSettingsDS::smk::setup") +# context("listDisclosureSettingsDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("listDisclosureSettingsDS::smk") +# context("listDisclosureSettingsDS::smk") test_that("simple listDisclosureSettingsDS", { res <- listDisclosureSettingsDS() @@ -70,6 +71,6 @@ test_that("simple listDisclosureSettingsDS", { # Done # -context("listDisclosureSettingsDS::smk::shutdown") +# context("listDisclosureSettingsDS::smk::shutdown") -context("listDisclosureSettingsDS::smk::done") +# context("listDisclosureSettingsDS::smk::done") diff --git a/tests/testthat/test-smk-lsDS.R b/tests/testthat/test-smk-lsDS.R index 077ee9fe..b96eb0ec 100644 --- a/tests/testthat/test-smk-lsDS.R +++ b/tests/testthat/test-smk-lsDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("lsDS::smk::setup") +# context("lsDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("lsDS::smk::simple") +# context("lsDS::smk::simple") test_that("simple lsDS", { .GlobalEnv$test.obj <- "value" @@ -36,7 +37,7 @@ test_that("simple lsDS", { expect_true("test.obj" %in% res$objects.found) }) -context("lsDS::smk::simple") +# context("lsDS::smk::simple") test_that("simple lsDS", { .GlobalEnv$test.obj <- "value" @@ -58,6 +59,6 @@ test_that("simple lsDS", { # Done # -context("lsDS::smk::shutdown") +# context("lsDS::smk::shutdown") -context("lsDS::smk::done") +# context("lsDS::smk::done") diff --git a/tests/testthat/test-smk-meanDS.R b/tests/testthat/test-smk-meanDS.R index befc82ba..e6d81a73 100644 --- a/tests/testthat/test-smk-meanDS.R +++ b/tests/testthat/test-smk-meanDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("meanDS::smk::setup") +# context("meanDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("meanDS::smk::numeric") +# context("meanDS::smk::numeric") test_that("numeric meanDS", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) @@ -40,7 +41,7 @@ test_that("numeric meanDS", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("meanDS::smk::numeric with NA") +# context("meanDS::smk::numeric with NA") test_that("numeric meanDS, with NA", { input <- c(0.0, NA, 2.0, NA, 4.0) @@ -60,7 +61,7 @@ test_that("numeric meanDS, with NA", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("meanDS::smk::numeric with all NA") +# context("meanDS::smk::numeric with all NA") test_that("numeric meanDS, with all NA", { input <- c(NA, NA, NA, NA, NA) @@ -84,6 +85,6 @@ test_that("numeric meanDS, with all NA", { # Done # -context("meanDS::smk::shutdown") +# context("meanDS::smk::shutdown") -context("meanDS::smk::done") +# context("meanDS::smk::done") diff --git a/tests/testthat/test-smk-messageDS.R b/tests/testthat/test-smk-messageDS.R index 871d2747..b92655e8 100644 --- a/tests/testthat/test-smk-messageDS.R +++ b/tests/testthat/test-smk-messageDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("messageDS::smk::setup") +# context("messageDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("messageDS::smk") +# context("messageDS::smk") test_that("simple messageDS", { expect_warning(base::rm("object"), "object 'object' not found", fixed = TRUE) @@ -86,6 +87,6 @@ test_that("simple messageDS", { # Done # -context("messageDS::smk::shutdown") +# context("messageDS::smk::shutdown") -context("messageDS::smk::done") +# context("messageDS::smk::done") diff --git a/tests/testthat/test-smk-metadataDS.R b/tests/testthat/test-smk-metadataDS.R index 1c4a3dab..4b0ab042 100644 --- a/tests/testthat/test-smk-metadataDS.R +++ b/tests/testthat/test-smk-metadataDS.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, 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. @@ -12,7 +12,7 @@ # Set up # -context("metadataDS::smk::setup") +# context("metadataDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +20,7 @@ set.standard.disclosure.settings() # Tests # -context("metadataDS::smk::list") +# context("metadataDS::smk::list") test_that("simple metadataDS, list of values", { input <- list(v1 = 0.0, v2 = 1.0) @@ -36,7 +36,7 @@ test_that("simple metadataDS, list of values", { expect_true("v2" %in% res$names) }) -context("metadataDS::smk::list field") +# context("metadataDS::smk::list field") test_that("simple metadataDS, list of vectors", { input <- list(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -50,6 +50,6 @@ test_that("simple metadataDS, list of vectors", { # Done # -context("metadataDS::smk::shutdown") +# context("metadataDS::smk::shutdown") -context("metadataDS::smk::done") +# context("metadataDS::smk::done") diff --git a/tests/testthat/test-smk-miceDS.R b/tests/testthat/test-smk-miceDS.R index 3c5af832..4f49f52b 100644 --- a/tests/testthat/test-smk-miceDS.R +++ b/tests/testthat/test-smk-miceDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("miceDS::smk::setup") +# context("miceDS::smk::setup") # # Tests # -context("miceDS::smk") +# context("miceDS::smk") test_that("miceDS", { load(file = 'data_files/CNSIM/CNSIM1.rda') @@ -53,6 +54,6 @@ test_that("miceDS", { # Done # -context("miceDS::smk::shutdown") +# context("miceDS::smk::shutdown") -context("miceDS::smk::done") +# context("miceDS::smk::done") diff --git a/tests/testthat/test-smk-minMaxRandDS.R b/tests/testthat/test-smk-minMaxRandDS.R index e5a9fe77..0e057e5a 100644 --- a/tests/testthat/test-smk-minMaxRandDS.R +++ b/tests/testthat/test-smk-minMaxRandDS.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, 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. @@ -12,7 +12,7 @@ # Set up # -context("minMaxRandDS::smk::setup") +# context("minMaxRandDS::smk::setup") # # Tests @@ -33,6 +33,6 @@ test_that("minMaxRandDS", { # Done # -context("minMaxRandDS::smk::shutdown") +# context("minMaxRandDS::smk::shutdown") -context("minMaxRandDS::smk::done") +# context("minMaxRandDS::smk::done") diff --git a/tests/testthat/test-smk-namesDS.R b/tests/testthat/test-smk-namesDS.R index 238c26d3..dbc5f3b1 100644 --- a/tests/testthat/test-smk-namesDS.R +++ b/tests/testthat/test-smk-namesDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("namesDS::smk::setup") +# context("namesDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("namesDS::smk::list of atoms") +# context("namesDS::smk::list of atoms") test_that("simple namesDS, data.frame", { input <- list(v1 = 0.0, v2 = 1.0) @@ -32,7 +33,7 @@ test_that("simple namesDS, data.frame", { expect_true("v2" %in% res) }) -context("namesDS::smk::list of vectors") +# context("namesDS::smk::list of vectors") test_that("simple namesDS, data.matrix", { input <- list(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -48,6 +49,6 @@ test_that("simple namesDS, data.matrix", { # Done # -context("namesDS::smk::shutdown") +# context("namesDS::smk::shutdown") -context("namesDS::smk::done") +# context("namesDS::smk::done") diff --git a/tests/testthat/test-smk-numNaDS.R b/tests/testthat/test-smk-numNaDS.R index 5de3dc46..c77db4ed 100644 --- a/tests/testthat/test-smk-numNaDS.R +++ b/tests/testthat/test-smk-numNaDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("numNaDS::smk::setup") +# context("numNaDS::smk::setup") # # Tests # -context("numNaDS::smk::simple") +# context("numNaDS::smk::simple") test_that("simple numNaDS", { input <- c(NA, 1, NA, 2, NA) @@ -43,6 +44,6 @@ test_that("simple numNaDS", { # Done # -context("numNaDS::smk::shutdown") +# context("numNaDS::smk::shutdown") -context("numNaDS::smk::done") +# context("numNaDS::smk::done") diff --git a/tests/testthat/test-smk-quantileMeanDS.R b/tests/testthat/test-smk-quantileMeanDS.R index 7ca9ac18..33eb0c6f 100644 --- a/tests/testthat/test-smk-quantileMeanDS.R +++ b/tests/testthat/test-smk-quantileMeanDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("quantileMeanDS::smk::setup") +# context("quantileMeanDS::smk::setup") # # Tests # -context("quantileMeanDS::smk") +# context("quantileMeanDS::smk") test_that("numeric quantileMeanDS", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) @@ -49,7 +50,7 @@ test_that("numeric quantileMeanDS", { expect_equal(res.names[[8]], "Mean") }) -context("quantileMeanDS::smk::with NA") +# context("quantileMeanDS::smk::with NA") test_that("numeric quantileMeanDS, with NA", { input <- c(0.0, NA, 2.0, NA, 4.0) @@ -84,6 +85,6 @@ test_that("numeric quantileMeanDS, with NA", { # Done # -context("quantileMeanDS::smk::shutdown") +# context("quantileMeanDS::smk::shutdown") -context("quantileMeanDS::smk::done") +# context("quantileMeanDS::smk::done") diff --git a/tests/testthat/test-smk-rBinomDS.R b/tests/testthat/test-smk-rBinomDS.R index d52ff3e7..9cff07d0 100644 --- a/tests/testthat/test-smk-rBinomDS.R +++ b/tests/testthat/test-smk-rBinomDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("rBinomDS::smk::setup") +# context("rBinomDS::smk::setup") # # Tests # -context("rBinomDS::smk::simple") +# context("rBinomDS::smk::simple") test_that("simple rBinomDS, by name", { n <- 8 size <- 32 @@ -61,6 +62,6 @@ test_that("simple rBinomDS, direct", { # Done # -context("rBinomDS::smk::shutdown") +# context("rBinomDS::smk::shutdown") -context("rBinomDS::smk::done") +# context("rBinomDS::smk::done") diff --git a/tests/testthat/test-smk-rNormDS.R b/tests/testthat/test-smk-rNormDS.R index c5b62afc..484ef851 100644 --- a/tests/testthat/test-smk-rNormDS.R +++ b/tests/testthat/test-smk-rNormDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("rNormDS::smk::setup") +# context("rNormDS::smk::setup") # # Tests # -context("rNormDS::smk::simple") +# context("rNormDS::smk::simple") test_that("simple rNormDS, by name", { n <- 8 mean <- 32.0 @@ -61,6 +62,6 @@ test_that("simple rNormDS, direct", { # Done # -context("rNormDS::smk::shutdown") +# context("rNormDS::smk::shutdown") -context("rNormDS::smk::done") +# context("rNormDS::smk::done") diff --git a/tests/testthat/test-smk-rPoisDS.R b/tests/testthat/test-smk-rPoisDS.R index a5d5c1fd..c2cf55bf 100644 --- a/tests/testthat/test-smk-rPoisDS.R +++ b/tests/testthat/test-smk-rPoisDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("rPoisDS::smk::setup") +# context("rPoisDS::smk::setup") # # Tests # -context("rPoisDS::smk::simple") +# context("rPoisDS::smk::simple") test_that("simple rPoisDS, by name", { n <- 8 lambda <- 32 @@ -59,6 +60,6 @@ test_that("simple rPoisDS, direct", { # Done # -context("rPoisDS::smk::shutdown") +# context("rPoisDS::smk::shutdown") -context("rPoisDS::smk::done") +# context("rPoisDS::smk::done") diff --git a/tests/testthat/test-smk-rUnifDS.R b/tests/testthat/test-smk-rUnifDS.R index a0e8d306..87c208c4 100644 --- a/tests/testthat/test-smk-rUnifDS.R +++ b/tests/testthat/test-smk-rUnifDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("rUnifDS::smk::setup") +# context("rUnifDS::smk::setup") # # Tests # -context("rUnifDS::smk::simple") +# context("rUnifDS::smk::simple") test_that("simple rUnifDS, by name", { n <- 8 min <- 2 @@ -61,6 +62,6 @@ test_that("simple rUnifDS, direct", { # Done # -context("rUnifDS::smk::shutdown") +# context("rUnifDS::smk::shutdown") -context("rUnifDS::smk::done") +# context("rUnifDS::smk::done") diff --git a/tests/testthat/test-smk-rangeDS.R b/tests/testthat/test-smk-rangeDS.R index ef04d6b1..c59c9d32 100644 --- a/tests/testthat/test-smk-rangeDS.R +++ b/tests/testthat/test-smk-rangeDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("rangeDS::smk::setup") +# context("rangeDS::smk::setup") set.random.seed.setting(1234) @@ -20,7 +21,7 @@ set.random.seed.setting(1234) # Tests # -context("rangeDS::smk::without NAs") +# context("rangeDS::smk::without NAs") test_that("numeric rangeDS", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0, 4.0, 3.0, 2.0, 1.0, 0.0) @@ -32,7 +33,7 @@ test_that("numeric rangeDS", { expect_equal(res[2], 4.12446, tolerance = 1e-6) }) -context("rangeDS::smk::with NAs") +# context("rangeDS::smk::with NAs") test_that("character rangeDS", { input <- c(0.0, NA, 2.0, NA, 4.0, NA, 3.0, NA, 1.0, NA) @@ -48,6 +49,6 @@ test_that("character rangeDS", { # Done # -context("rangeDS::smk::shutdown") +# context("rangeDS::smk::shutdown") -context("rangeDS::smk::done") +# context("rangeDS::smk::done") diff --git a/tests/testthat/test-smk-rbindDS.R b/tests/testthat/test-smk-rbindDS.R index 846b31bc..7f757a1e 100644 --- a/tests/testthat/test-smk-rbindDS.R +++ b/tests/testthat/test-smk-rbindDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("rbindDS::smk::setup") +# context("rbindDS::smk::setup") # # Tests # -context("rbindDS::smk::simple") +# context("rbindDS::smk::simple") test_that("simple rbindDS", { inputs <- 'input1, input2' input1 <- c(0.0, 1.0, 2.0, 3.0) @@ -61,6 +62,6 @@ test_that("simple rbindDS", { # Done # -context("rbindDS::smk::shutdown") +# context("rbindDS::smk::shutdown") -context("rbindDS::smk::done") +# context("rbindDS::smk::done") diff --git a/tests/testthat/test-smk-recodeLevelsDS.R b/tests/testthat/test-smk-recodeLevelsDS.R index 2eaef21b..9e365836 100644 --- a/tests/testthat/test-smk-recodeLevelsDS.R +++ b/tests/testthat/test-smk-recodeLevelsDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("recodeLevelsDS::smk::setup") +# context("recodeLevelsDS::smk::setup") # # Tests @@ -41,6 +42,6 @@ test_that("simple recodeLevelsDS", { # Done # -context("recodeLevelsDS::smk::shutdown") +# context("recodeLevelsDS::smk::shutdown") -context("recodeLevelsDS::smk::done") +# context("recodeLevelsDS::smk::done") diff --git a/tests/testthat/test-smk-recodeValuesDS.R b/tests/testthat/test-smk-recodeValuesDS.R index 14e7cb98..09b9e2f3 100644 --- a/tests/testthat/test-smk-recodeValuesDS.R +++ b/tests/testthat/test-smk-recodeValuesDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("recodeValuesDS::smk::setup") +# context("recodeValuesDS::smk::setup") set.standard.disclosure.settings() @@ -126,6 +127,6 @@ test_that("simple recodeValuesDS, character input with missings", { # Done # -context("recodeValuesDS::smk::shutdown") +# context("recodeValuesDS::smk::shutdown") -context("recodeValuesDS::smk::done") +# context("recodeValuesDS::smk::done") diff --git a/tests/testthat/test-smk-replaceNaDS.R b/tests/testthat/test-smk-replaceNaDS.R index f092b9cd..b2b4cfff 100644 --- a/tests/testthat/test-smk-replaceNaDS.R +++ b/tests/testthat/test-smk-replaceNaDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("replaceNaDS::smk::setup") +# context("replaceNaDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("replaceNaDS::smk") +# context("replaceNaDS::smk") 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) @@ -43,6 +44,6 @@ test_that("simple replaceNaDS", { # Done # -context("replaceNaDS::smk::shutdown") +# context("replaceNaDS::smk::shutdown") -context("replaceNaDS::smk::done") +# context("replaceNaDS::smk::done") diff --git a/tests/testthat/test-smk-rmDS.R b/tests/testthat/test-smk-rmDS.R index 7bab6da2..aae9c5f1 100644 --- a/tests/testthat/test-smk-rmDS.R +++ b/tests/testthat/test-smk-rmDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("rmDS::smk::setup") +# context("rmDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("rmDS::smk::single") +# context("rmDS::smk::single") test_that("single rmDS", { expect_false(exists("input")) @@ -40,7 +41,7 @@ test_that("single rmDS", { expect_equal(res$problem.objects, "", fixed = TRUE) }) -context("rmDS::smk::multiple") +# context("rmDS::smk::multiple") test_that("multiple rmDS", { expect_false(exists("input1")) expect_false(exists("input2")) @@ -65,7 +66,7 @@ test_that("multiple rmDS", { expect_equal(res$problem.objects, "", fixed = TRUE) }) -context("rmDS::smk::single missing") +# context("rmDS::smk::single missing") test_that("single missing rmDS", { expect_false(exists("input")) @@ -82,7 +83,7 @@ test_that("single missing rmDS", { }) -context("rmDS::smk::multiple missing") +# context("rmDS::smk::multiple missing") test_that("multiple missing rmDS", { expect_false(exists("input1")) expect_false(exists("input2")) @@ -100,7 +101,7 @@ test_that("multiple missing rmDS", { expect_equal(res$problem.objects, "", fixed = TRUE) }) -context("rmDS::smk::multiple mixed") +# context("rmDS::smk::multiple mixed") test_that("multiple mixed rmDS", { expect_false(exists("input1")) expect_false(exists("input2")) @@ -124,6 +125,6 @@ test_that("multiple mixed rmDS", { # Done # -context("rmDS::smk::shutdown") +# context("rmDS::smk::shutdown") -context("rmDS::smk::done") +# context("rmDS::smk::done") diff --git a/tests/testthat/test-smk-rowColCalcDS.R b/tests/testthat/test-smk-rowColCalcDS.R index c951a73b..615aa2ff 100644 --- a/tests/testthat/test-smk-rowColCalcDS.R +++ b/tests/testthat/test-smk-rowColCalcDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("rowColCalcDS::smk::setup") +# context("rowColCalcDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("rowColCalcDS::smk") +# context("rowColCalcDS::smk") test_that("simple rowColCalcDS, operation 1", { input <- matrix(c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0), ncol = 2) @@ -77,6 +78,6 @@ test_that("simple rowColCalcDS, operation 4", { # Done # -context("rowColCalcDS::smk::shutdown") +# context("rowColCalcDS::smk::shutdown") -context("rowColCalcDS::smk::done") +# context("rowColCalcDS::smk::done") diff --git a/tests/testthat/test-smk-sampleDS.R b/tests/testthat/test-smk-sampleDS.R index b30f86e6..e3927518 100644 --- a/tests/testthat/test-smk-sampleDS.R +++ b/tests/testthat/test-smk-sampleDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("sampleDS::smk::setup") +# context("sampleDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("sampleDS::smk::simple") +# context("sampleDS::smk::simple") test_that("simple sampleDS", { x <- c(1:32) size <- 16 @@ -49,6 +50,6 @@ test_that("simple sampleDS", { # Done # -context("sampleDS::smk::shutdown") +# context("sampleDS::smk::shutdown") -context("sampleDS::smk::done") +# context("sampleDS::smk::done") diff --git a/tests/testthat/test-smk-seqDS.R b/tests/testthat/test-smk-seqDS.R index b0660b58..7cdd62eb 100644 --- a/tests/testthat/test-smk-seqDS.R +++ b/tests/testthat/test-smk-seqDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("seqDS::smk::setup") +# context("seqDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("seqDS::smk") +# context("seqDS::smk") test_that("simple seqDS", { FROM.value.char <- "1" TO.value.char <- "12" @@ -121,6 +122,6 @@ test_that("simple seqDS", { # Done # -context("seqDS::smk::shutdown") +# context("seqDS::smk::shutdown") -context("seqDS::smk::done") +# context("seqDS::smk::done") diff --git a/tests/testthat/test-smk-setFilterDS.R b/tests/testthat/test-smk-setFilterDS.R index 2b32a6f9..93e54b7e 100644 --- a/tests/testthat/test-smk-setFilterDS.R +++ b/tests/testthat/test-smk-setFilterDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("setFilterDS::smk::setup") +# context("setFilterDS::smk::setup") set.standard.disclosure.settings @@ -20,7 +21,7 @@ set.standard.disclosure.settings # Tests # -context("setFilterDS::smk::simple") +# context("setFilterDS::smk::simple") test_that("simple setFilterDS", { res <- setFilterDS() @@ -43,6 +44,6 @@ test_that("simple setFilterDS", { # Done # -context("setFilterDS::smk::shutdown") +# context("setFilterDS::smk::shutdown") -context("setFilterDS::smk::done") +# context("setFilterDS::smk::done") diff --git a/tests/testthat/test-smk-setSeedDS.R b/tests/testthat/test-smk-setSeedDS.R index 6db3d8bc..0cdbf2e9 100644 --- a/tests/testthat/test-smk-setSeedDS.R +++ b/tests/testthat/test-smk-setSeedDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("setSeedDS::smk::setup") +# context("setSeedDS::smk::setup") # # Tests # -context("setSeedDS::smk::simple") +# context("setSeedDS::smk::simple") test_that("simple setSeedDS", { seedtext <- "19" kind <- NULL @@ -35,6 +36,6 @@ test_that("simple setSeedDS", { # Done # -context("setSeedDS::smk::shutdown") +# context("setSeedDS::smk::shutdown") -context("setSeedDS::smk::done") +# context("setSeedDS::smk::done") diff --git a/tests/testthat/test-smk-skewnessDS1.R b/tests/testthat/test-smk-skewnessDS1.R index 76f8d4fd..bfd0cceb 100644 --- a/tests/testthat/test-smk-skewnessDS1.R +++ b/tests/testthat/test-smk-skewnessDS1.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("skewnessDS1::smk::setup") +# context("skewnessDS1::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("skewnessDS1::smk::method 1") +# context("skewnessDS1::smk::method 1") test_that("simple skewnessDS1, method 1", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) @@ -36,7 +37,7 @@ test_that("simple skewnessDS1, method 1", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("skewnessDS1::smk::method 2") +# context("skewnessDS1::smk::method 2") test_that("simple skewnessDS1, method 2", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) @@ -52,7 +53,7 @@ test_that("simple skewnessDS1, method 2", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("skewnessDS1::smk::method 3") +# context("skewnessDS1::smk::method 3") test_that("simple skewnessDS1, method 3", { input <- c(0.0, 1.0, 1.0, 1.0, 2.0, 2.0, 2.0, 3.0, 4.0) @@ -72,6 +73,6 @@ test_that("simple skewnessDS1, method 3", { # Done # -context("skewnessDS1::smk::shutdown") +# context("skewnessDS1::smk::shutdown") -context("skewnessDS1::smk::done") +# context("skewnessDS1::smk::done") diff --git a/tests/testthat/test-smk-skewnessDS2.R b/tests/testthat/test-smk-skewnessDS2.R index 1966109d..9e59061d 100644 --- a/tests/testthat/test-smk-skewnessDS2.R +++ b/tests/testthat/test-smk-skewnessDS2.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("skewnessDS2::smk::setup") +# context("skewnessDS2::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("skewnessDS2::smk") +# context("skewnessDS2::smk") test_that("simple skewnessDS2", { input <- c(1.0, 2.0, 2.0, 3.0, 3.0) global.mean <- 2.5 @@ -43,6 +44,6 @@ test_that("simple skewnessDS2", { # Done # -context("skewnessDS2::smk::shutdown") +# context("skewnessDS2::smk::shutdown") -context("skewnessDS2::smk::done") +# context("skewnessDS2::smk::done") diff --git a/tests/testthat/test-smk-sqrtDS.R b/tests/testthat/test-smk-sqrtDS.R index 2689d375..fe9ac9eb 100644 --- a/tests/testthat/test-smk-sqrtDS.R +++ b/tests/testthat/test-smk-sqrtDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("sqrtDS::smk::setup") +# context("sqrtDS::smk::setup") # # Tests # -context("sqrtDS::smk::special") +# context("sqrtDS::smk::special") test_that("simple sqrtDS, NA", { input <- NA @@ -59,7 +60,7 @@ test_that("simple sqrtDS, -Inf", { expect_true(is.nan(res)) }) -context("sqrtDS::smk::numeric") +# context("sqrtDS::smk::numeric") test_that("simple sqrtDS, numeric 0.0", { input <- 0.0 @@ -90,7 +91,7 @@ test_that("simple sqrtDS, numeric -10.0", { expect_true(is.nan(res)) }) -context("sqrtDS::smk::integer") +# context("sqrtDS::smk::integer") test_that("simple sqrtDS, integer 0L", { input <- 0L @@ -121,7 +122,7 @@ test_that("simple sqrtDS, integer -10L", { expect_true(is.nan(res)) }) -context("sqrtDS::smk::special vector") +# context("sqrtDS::smk::special vector") test_that("simple sqrtDS", { input <- c(NA, NaN, Inf, -Inf) @@ -134,7 +135,7 @@ test_that("simple sqrtDS", { expect_true(is.nan(res[4])) }) -context("sqrtDS::smk::numeric vector") +# context("sqrtDS::smk::numeric vector") test_that("simple sqrtDS", { input <- c(0.0, 4.0, 9.0, -10.0, -50.0, -20.0) @@ -150,7 +151,7 @@ test_that("simple sqrtDS", { expect_true(is.nan(res[6])) }) -context("sqrtDS::smk::integer vector") +# context("sqrtDS::smk::integer vector") test_that("simple sqrtDS", { input <- c(0L, 4L, 9L, -10L, -50L, -20L) @@ -170,6 +171,6 @@ test_that("simple sqrtDS", { # Done # -context("sqrtDS::smk::shutdown") +# context("sqrtDS::smk::shutdown") -context("sqrtDS::smk::done") +# context("sqrtDS::smk::done") diff --git a/tests/testthat/test-smk-subsetByClassDS.R b/tests/testthat/test-smk-subsetByClassDS.R index 8de5114b..82ccab5d 100644 --- a/tests/testthat/test-smk-subsetByClassDS.R +++ b/tests/testthat/test-smk-subsetByClassDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("subsetByClassDS::smk::setup") +# context("subsetByClassDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("subsetByClassDS::smk") +# context("subsetByClassDS::smk") test_that("simple subsetByClassDS, data.frame, unspecified variables", { data <- data.frame(v1 = factor(c(0, 0, 0, 1, 1, 1, 2, 1, 2, 2)), v2 = c(4.0, 0.0, 3.0, 1.0, 2.0, 2.0, 1.0, 3.0, 0.0, 4.0), v3 = c(1:10), v4 = c(1:10)) variables <- NULL @@ -82,6 +83,6 @@ test_that("simple subsetByClassDS, factor vector, specified variables", { # Done # -context("subsetByClassDS::smk::shutdown") +# context("subsetByClassDS::smk::shutdown") -context("subsetByClassDS::smk::done") +# context("subsetByClassDS::smk::done") diff --git a/tests/testthat/test-smk-subsetDS.R b/tests/testthat/test-smk-subsetDS.R index f34119c4..53d291c4 100644 --- a/tests/testthat/test-smk-subsetDS.R +++ b/tests/testthat/test-smk-subsetDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("subsetDS::smk::setup") +# context("subsetDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("subsetDS::smk") +# context("subsetDS::smk") test_that("simple subsetDS, no NAs", { data <- data.frame(v1 = c(0, 0, 1, 1, 2, 2, 3, 3, 4, 4), v2 = c(4.0, 0.0, 3.0, 1.0, 2.0, 2.0, 1.0, 3.0, 0.0, 4.0)) complt <- FALSE @@ -120,6 +121,6 @@ test_that("simple subsetDS, NAs, complete.case TRUE", { # Done # -context("subsetDS::smk::shutdown") +# context("subsetDS::smk::shutdown") -context("subsetDS::smk::done") +# context("subsetDS::smk::done") diff --git a/tests/testthat/test-smk-tapplyDS.R b/tests/testthat/test-smk-tapplyDS.R index 5824713d..7925b49a 100644 --- a/tests/testthat/test-smk-tapplyDS.R +++ b/tests/testthat/test-smk-tapplyDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("tapplyDS::smk::setup") +# context("tapplyDS::smk::setup") set.standard.disclosure.settings() @@ -161,6 +162,6 @@ test_that("simple tapplyDS, quantile", { # Done # -context("tapplyDS::smk::shutdown") +# context("tapplyDS::smk::shutdown") -context("tapplyDS::smk::done") +# context("tapplyDS::smk::done") diff --git a/tests/testthat/test-smk-tapplyDS.assign.R b/tests/testthat/test-smk-tapplyDS.assign.R index 90c57654..7d899a2e 100644 --- a/tests/testthat/test-smk-tapplyDS.assign.R +++ b/tests/testthat/test-smk-tapplyDS.assign.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("tapplyDS.assign::smk::setup") +# context("tapplyDS.assign::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("tapplyDS.assign::smk::simple") +# context("tapplyDS.assign::smk::simple") test_that("simple tapplyDS.assign", { x <- c(1, 2, 1, 2, 1, 2, 1, 2) index <- factor(c(1, 2, 1, 2, 1, 2, 1, 2)) @@ -54,6 +55,6 @@ test_that("simple tapplyDS.assign", { # Done # -context("tapplyDS.assign::smk::shutdown") +# context("tapplyDS.assign::smk::shutdown") -context("tapplyDS.assign::smk::done") +# context("tapplyDS.assign::smk::done") diff --git a/tests/testthat/test-smk-testObjExistsDS.R b/tests/testthat/test-smk-testObjExistsDS.R index 6dd2780d..705948d0 100644 --- a/tests/testthat/test-smk-testObjExistsDS.R +++ b/tests/testthat/test-smk-testObjExistsDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("testObjExistsDS::smk::setup") +# context("testObjExistsDS::smk::setup") # # Tests # -context("testObjExistsDS::smk::character") +# context("testObjExistsDS::smk::character") test_that("simple testObjExistsDS, character", { input <- "value" @@ -41,7 +42,7 @@ test_that("simple testObjExistsDS, character vector", { expect_equal(res$test.obj.class, "character") }) -context("testObjExistsDS::smk::integer") +# context("testObjExistsDS::smk::integer") test_that("simple testObjExistsDS, integer", { input <- 1L @@ -64,7 +65,7 @@ test_that("simple testObjExistsDS, integer vector", { expect_equal(res$test.obj.class, "integer") }) -context("testObjExistsDS::smk::numeric") +# context("testObjExistsDS::smk::numeric") test_that("simple testObjExistsDS, numeric", { input <- 1.1 @@ -87,7 +88,7 @@ test_that("simple testObjExistsDS, numeric vector", { expect_equal(res$test.obj.class, "numeric") }) -context("testObjExistsDS::smk::logical") +# context("testObjExistsDS::smk::logical") test_that("simple testObjExistsDS, logical, FALSE", { input <- FALSE @@ -121,7 +122,7 @@ test_that("simple testObjExistsDS, logical vector", { expect_equal(res$test.obj.class, "logical") }) -context("testObjExistsDS::smk::data.frame") +# context("testObjExistsDS::smk::data.frame") test_that("simple testObjExistsDS, data.frame", { input <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0)) @@ -133,7 +134,7 @@ test_that("simple testObjExistsDS, data.frame", { expect_equal(res$test.obj.class, "data.frame") }) -context("testObjExistsDS::smk::array") +# context("testObjExistsDS::smk::array") test_that("simple testObjExistsDS, array", { input <- array(c(0.0, 1.0, 2.0, 3.0, 4.0)) @@ -145,7 +146,7 @@ test_that("simple testObjExistsDS, array", { expect_equal(res$test.obj.class, "array") }) -context("testObjExistsDS::smk::matrix") +# context("testObjExistsDS::smk::matrix") test_that("simple testObjExistsDS, matrix", { input <- matrix(c(0.0, 1.0, 2.0, 3.0, 4.0)) @@ -167,7 +168,7 @@ test_that("simple testObjExistsDS, matrix", { } }) -context("testObjExistsDS::smk::data.matrix") +# context("testObjExistsDS::smk::data.matrix") test_that("simple testObjExistsDS, data.matrix", { input <- data.matrix(data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0))) @@ -190,7 +191,7 @@ test_that("simple testObjExistsDS, data.matrix", { } }) -context("testObjExistsDS::smk::date") +# context("testObjExistsDS::smk::date") test_that("simple testObjExistsDS, date", { input <- Sys.Date() @@ -202,7 +203,7 @@ test_that("simple testObjExistsDS, date", { expect_equal(res$test.obj.class, "Date") }) -context("testObjExistsDS::smk::formula") +# context("testObjExistsDS::smk::formula") test_that("simple testObjExistsDS, formula", { input <- X ~ A + B @@ -214,7 +215,7 @@ test_that("simple testObjExistsDS, formula", { expect_equal(res$test.obj.class, "formula") }) -context("testObjExistsDS::smk::environment") +# context("testObjExistsDS::smk::environment") test_that("simple testObjExistsDS, environment", { input <- environment() @@ -226,7 +227,7 @@ test_that("simple testObjExistsDS, environment", { expect_equal(res$test.obj.class, "environment") }) -context("testObjExistsDS::smk::NA") +# context("testObjExistsDS::smk::NA") test_that("special testObjExistsDS, NA", { input <- NA @@ -238,7 +239,7 @@ test_that("special testObjExistsDS, NA", { expect_equal(res$test.obj.class, "logical") }) -context("testObjExistsDS::smk::NULL") +# context("testObjExistsDS::smk::NULL") test_that("special testObjExistsDS, NULL", { input <- NULL @@ -250,7 +251,7 @@ test_that("special testObjExistsDS, NULL", { expect_equal(res$test.obj.class, "NULL") }) -context("testObjExistsDS::smk::not exists") +# context("testObjExistsDS::smk::not exists") test_that("special testObjExistsDS, not exists", { res <- testObjExistsDS("XXXinputXXX") @@ -264,6 +265,6 @@ test_that("special testObjExistsDS, not exists", { # Done # -context("testObjExistsDS::smk::shutdown") +# context("testObjExistsDS::smk::shutdown") -context("testObjExistsDS::smk::done") +# context("testObjExistsDS::smk::done") diff --git a/tests/testthat/test-smk-unListDS.R b/tests/testthat/test-smk-unListDS.R index 316806d3..b8f814fe 100644 --- a/tests/testthat/test-smk-unListDS.R +++ b/tests/testthat/test-smk-unListDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("unListDS::smk::setup") +# context("unListDS::smk::setup") # # Tests # -context("unListDS::smk::simple") +# context("unListDS::smk::simple") test_that("simple unListDS", { input <- list(v1 = c(1, 2, 3), v2 = c(4, 5, 6)) @@ -49,6 +50,6 @@ test_that("simple unListDS", { # Done # -context("unListDS::smk::shutdown") +# context("unListDS::smk::shutdown") -context("unListDS::smk::done") +# context("unListDS::smk::done") diff --git a/tests/testthat/test-smk-uniqueDS.R b/tests/testthat/test-smk-uniqueDS.R index 2bad97cf..3f4b908c 100644 --- a/tests/testthat/test-smk-uniqueDS.R +++ b/tests/testthat/test-smk-uniqueDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,13 +13,13 @@ # Set up # -context("uniqueDS::smk::setup") +# context("uniqueDS::smk::setup") # # Tests # -context("uniqueDS::smk::simple for vector") +# context("uniqueDS::smk::simple for vector") test_that("simple uniqueDS for vector", { input <- c(1, 2, 3, 2, 3, 6) @@ -32,7 +33,7 @@ test_that("simple uniqueDS for vector", { expect_equal(res[[4]], 6) }) -context("uniqueDS::smk::simple for vector") +# context("uniqueDS::smk::simple for vector") test_that("simple uniqueDS for list", { input <- list(a=1, b=2, c=3, d=2, e=3, f=6) @@ -52,6 +53,6 @@ test_that("simple uniqueDS for list", { # Done # -context("uniqueDS::smk::shutdown") +# context("uniqueDS::smk::shutdown") -context("uniqueDS::smk::done") +# context("uniqueDS::smk::done") diff --git a/tests/testthat/test-smk-varDS.R b/tests/testthat/test-smk-varDS.R index 34ba8670..517b8d8f 100644 --- a/tests/testthat/test-smk-varDS.R +++ b/tests/testthat/test-smk-varDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # 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. @@ -12,7 +13,7 @@ # Set up # -context("varDS::smk::setup") +# context("varDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +21,7 @@ set.standard.disclosure.settings() # Tests # -context("varDS::smk::numeric") +# context("varDS::smk::numeric") test_that("numeric varDS", { input <- c(0.0, 1.0, 2.0, 3.0, 4.0) @@ -42,7 +43,7 @@ test_that("numeric varDS", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("varDS::smk::numeric with NA") +# context("varDS::smk::numeric with NA") test_that("numeric varDS, with NA", { input <- c(0.0, NA, 2.0, NA, 4.0) @@ -64,7 +65,7 @@ test_that("numeric varDS, with NA", { expect_equal(res$ValidityMessage, "VALID ANALYSIS") }) -context("varDS::smk::numeric with all NA") +# context("varDS::smk::numeric with all NA") test_that("numeric varDS, with all NA", { input <- c(NA, NA, NA, NA, NA) @@ -90,6 +91,6 @@ test_that("numeric varDS, with all NA", { # Done # -context("varDS::smk::shutdown") +# context("varDS::smk::shutdown") -context("varDS::smk::done") +# context("varDS::smk::done") diff --git a/tests/testthat/test-smk-vectorDS.R b/tests/testthat/test-smk-vectorDS.R index d6ef7ff2..3d4b48c6 100644 --- a/tests/testthat/test-smk-vectorDS.R +++ b/tests/testthat/test-smk-vectorDS.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 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. @@ -12,7 +12,7 @@ # Set up # -context("vectorDS::smk::setup") +# context("vectorDS::smk::setup") set.standard.disclosure.settings() @@ -20,7 +20,7 @@ set.standard.disclosure.settings() # Tests # -context("vectorDS::smk::numeric list") +# context("vectorDS::smk::numeric list") test_that("numeric list vectorDS", { input <- list(a=0.0, b=1.0, c=2.0, d=3.0) @@ -34,7 +34,7 @@ test_that("numeric list vectorDS", { expect_equal(res[[4]], 3.0) }) -context("vectorDS::smk::character list") +# context("vectorDS::smk::character list") test_that("character list vectorDS", { input <- list(a="0.0", b="1.0", c="2.0", d="3.0") @@ -48,7 +48,7 @@ test_that("character list vectorDS", { expect_equal(res[[4]], "3.0") }) -context("vectorDS::smk::numeric list small") +# context("vectorDS::smk::numeric list small") test_that("single numeric list small vectorDS", { input <- list(a=0, b=1) @@ -60,7 +60,7 @@ test_that("single numeric list small vectorDS", { expect_equal(res[[2]], 1) }) -context("vectorDS::smk::empty list") +# context("vectorDS::smk::empty list") test_that("empty list vectorDS", { input <- list() @@ -74,6 +74,6 @@ test_that("empty list vectorDS", { # Done # -context("vectorDS::smk::shutdown") +# context("vectorDS::smk::shutdown") -context("vectorDS::smk::done") +# context("vectorDS::smk::done") From 809f7cbd38e5f8f1d26da78f388571ead725e94e Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 27 Oct 2025 12:31:18 +0000 Subject: [PATCH 13/22] Change version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d00d8a10..bc5e3973 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see 'citation("dsBase")'. -Version: 6.3.4 +Version: 6.3.5.9000 Authors@R: c(person(given = "Paul", family = "Burton", role = c("aut"), From 1e0b07f68864575ce302a04a065543720b5aea10 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 28 Oct 2025 12:43:39 +0000 Subject: [PATCH 14/22] Add "pull request template" to .Rbuildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 59863e10..0d7af444 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,3 +11,4 @@ ^\.circleci/config\.yml$ ^\.github$ ^cran-comments\.md$ +^pull_request_template‎$ From 511b95ddf134fcf80552fd4f5e51d9879547b32f Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 28 Oct 2025 14:35:40 +0000 Subject: [PATCH 15/22] Comment out 'context(...)' --- tests/testthat/test-smk-utils.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/testthat/test-smk-utils.R b/tests/testthat/test-smk-utils.R index de901962..77cf9c02 100644 --- a/tests/testthat/test-smk-utils.R +++ b/tests/testthat/test-smk-utils.R @@ -13,7 +13,7 @@ # Set up # -context("utils::smk::setup") +# context("utils::smk::setup") test_that(".loadServersideObject() returns existing object", { test_df <- data.frame(a = 1:3) result <- .loadServersideObject("test_df") @@ -42,5 +42,5 @@ test_that(".checkClass() throws informative error for wrong class", { ) }) -context("utils::smk::shutdown") -context("utils::smk::done") +# context("utils::smk::shutdown") +# context("utils::smk::done") From b6e7cb5b99473694af973d846dd3e8d085d60899 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 28 Oct 2025 17:36:06 +0000 Subject: [PATCH 16/22] Update for 'testthat' and other changes --- tests/testthat/test-smk-aucDS.R | 2 +- tests/testthat/test-smk-corTestDS.R | 14 +++++----- tests/testthat/test-smk-messageDS.R | 12 ++++---- tests/testthat/test-smk-miceDS.R | 16 +++++++---- tests/testthat/test-smk-rmDS.R | 40 +++++++++++++-------------- tests/testthat/test-smk-skewnessDS1.R | 2 +- 6 files changed, 45 insertions(+), 41 deletions(-) diff --git a/tests/testthat/test-smk-aucDS.R b/tests/testthat/test-smk-aucDS.R index 2e03ccdb..bcbbada1 100644 --- a/tests/testthat/test-smk-aucDS.R +++ b/tests/testthat/test-smk-aucDS.R @@ -32,7 +32,7 @@ test_that("aucDS", { expect_equal(class(res$AUC), "numeric") expect_equal(res$AUC, 0.6767515, tolerance=1e-07) expect_equal(class(res$se), "numeric") - expect_equal(res$se, 0.02065186, tolerance=1e-08) + expect_equal(res$se, 0.02065186, tolerance=1e-07) }) diff --git a/tests/testthat/test-smk-corTestDS.R b/tests/testthat/test-smk-corTestDS.R index 1314b933..b500a085 100644 --- a/tests/testthat/test-smk-corTestDS.R +++ b/tests/testthat/test-smk-corTestDS.R @@ -254,8 +254,8 @@ test_that("simple corTestDS, full, without na, kendall", { expect_equal(class(res$`Correlation test`$p.value), "numeric") expect_length(res$`Correlation test`$p.value, 1) - expect_equal(res$`Correlation test`$p.value[[1]], 4.96e-05) - + expect_equal(res$`Correlation test`$p.value[[1]], 4.960317e-05, tolerance = 1e-6) + expect_equal(class(res$`Correlation test`$estimate), "numeric") expect_length(res$`Correlation test`$estimate, 1) expect_equal(res$`Correlation test`$estimate[[1]], 1.0) @@ -346,7 +346,7 @@ test_that("simple corTestDS, some, kendall, without na, kendall", { expect_equal(class(res$`Correlation test`$p.value), "numeric") expect_length(res$`Correlation test`$p.value, 1) - expect_equal(res$`Correlation test`$p.value[[1]], 4.96e-05) + expect_equal(res$`Correlation test`$p.value[[1]], 4.960317e-05, tolerance = 1e-6) expect_equal(class(res$`Correlation test`$estimate), "numeric") expect_length(res$`Correlation test`$estimate, 1) @@ -440,7 +440,7 @@ test_that("simple corTestDS, full, without na, spearman", { expect_equal(class(res$`Correlation test`$p.value), "numeric") expect_length(res$`Correlation test`$p.value, 1) - expect_equal(res$`Correlation test`$p.value[[1]], 4.96e-05) + expect_equal(res$`Correlation test`$p.value[[1]], 4.960317e-05, tolerance = 1e-6) expect_equal(class(res$`Correlation test`$estimate), "numeric") expect_length(res$`Correlation test`$estimate, 1) @@ -486,7 +486,7 @@ test_that("simple corTestDS, neg. full, without na, spearman", { expect_equal(class(res$`Correlation test`$p.value), "numeric") expect_length(res$`Correlation test`$p.value, 1) - expect_equal(res$`Correlation test`$p.value[[1]], 4.96e-05) + expect_equal(res$`Correlation test`$p.value[[1]], 4.960317e-05, tolerance = 1e-6) expect_equal(class(res$`Correlation test`$estimate), "numeric") expect_length(res$`Correlation test`$estimate, 1) @@ -532,11 +532,11 @@ test_that("simple corTestDS, some, spearman, without na, spearman", { expect_equal(class(res$`Correlation test`$p.value), "numeric") expect_length(res$`Correlation test`$p.value, 1) - expect_equal(res$`Correlation test`$p.value[[1]], 4.96e-05) + expect_equal(res$`Correlation test`$p.value[[1]], 4.960317e-05, tolerance = 1e-6) expect_equal(class(res$`Correlation test`$estimate), "numeric") expect_length(res$`Correlation test`$estimate, 1) - expect_equal(res$`Correlation test`$estimate[[1]], 1.0) + expect_equal(res$`Correlation test`$estimate[[1]], 1.0, tolerance = 1e-6) expect_equal(class(res$`Correlation test`$null.value), "numeric") expect_length(res$`Correlation test`$null.value, 1) diff --git a/tests/testthat/test-smk-messageDS.R b/tests/testthat/test-smk-messageDS.R index b92655e8..91ec685b 100644 --- a/tests/testthat/test-smk-messageDS.R +++ b/tests/testthat/test-smk-messageDS.R @@ -29,7 +29,7 @@ test_that("simple messageDS", { expect_equal(class(res), "character") expect_length(res, 1) - expect_equal(res, "Error: the object does not exist in this datasource", fixed = TRUE) + expect_equal(res, "Error: the object does not exist in this datasource") }) test_that("simple messageDS", { @@ -39,7 +39,7 @@ test_that("simple messageDS", { expect_equal(class(res), "character") expect_length(res, 1) - expect_equal(res, "ALL OK: there are no studysideMessage(s) on this datasource", fixed = TRUE) + expect_equal(res, "ALL OK: there are no studysideMessage(s) on this datasource") }) test_that("simple messageDS", { @@ -49,7 +49,7 @@ test_that("simple messageDS", { expect_equal(class(res), "character") expect_length(res, 1) - expect_equal(res, "Outcome object is a list without names. So a studysideMessage may be hidden. Please check output is OK", fixed = TRUE) + expect_equal(res, "Outcome object is a list without names. So a studysideMessage may be hidden. Please check output is OK") }) @@ -60,7 +60,7 @@ test_that("simple messageDS", { expect_equal(class(res), "character") expect_length(res, 1) - expect_equal(res, "Outcome object is a list without names. So a studysideMessage may be hidden. Please check output is OK", fixed = TRUE) + expect_equal(res, "Outcome object is a list without names. So a studysideMessage may be hidden. Please check output is OK") }) test_that("simple messageDS", { @@ -70,7 +70,7 @@ test_that("simple messageDS", { expect_equal(class(res), "character") expect_length(res, 1) - expect_equal(res, "ALL OK: there are no studysideMessage(s) on this datasource", fixed = TRUE) + expect_equal(res, "ALL OK: there are no studysideMessage(s) on this datasource") }) test_that("simple messageDS", { @@ -80,7 +80,7 @@ test_that("simple messageDS", { expect_equal(class(res), "character") expect_length(res, 1) - expect_equal(res, "NOT ALL OK: there are studysideMessage(s) on this datasource", fixed = TRUE) + expect_equal(res, "NOT ALL OK: there are studysideMessage(s) on this datasource") }) # diff --git a/tests/testthat/test-smk-miceDS.R b/tests/testthat/test-smk-miceDS.R index 4f49f52b..86df2249 100644 --- a/tests/testthat/test-smk-miceDS.R +++ b/tests/testthat/test-smk-miceDS.R @@ -25,15 +25,19 @@ test_that("miceDS", { load(file = 'data_files/CNSIM/CNSIM1.rda') D <- study1 - res <- miceDS(data='D', m=1, maxit=5, method=NULL, post=NULL, predictorMatrix=NULL, seed=NA, - ncol.pred.mat=NULL, newobj_mids='mids_object', newobj_df='impSet') + expect_warning(res <- miceDS(data='D', m=1, maxit=5, method=NULL, post=NULL, predictorMatrix=NULL, seed=NA, + ncol.pred.mat=NULL, newobj_mids='mids_object', newobj_df='impSet'), "Number of logged events: 1") - expect_equal(class(res), "list") + expect_true(all(class(res) %in% c("list"))) + print(class(res)) expect_length(res, 3) - expect_true("character" %in% class(res$method)) + expect_true(all(class(res$method) %in% c("character"))) + print(class(res$method)) expect_equal(as.character(res$method), c("pmm","pmm","pmm","pmm","pmm","","","","","","polyreg")) - expect_true("matrix" %in% class(res$predictorMatrix)) - expect_true("array" %in% class(res$predictorMatrix)) + expect_true(all(class(res$predictorMatrix) %in% c("matrix array"))) + print(class(res$predictorMatrix)) + expect_true(all(class(res$predictorMatrix) %in% c("matrix array"))) + print(class(res$predictorMatrix)) expect_equal(as.numeric(res$predictorMatrix[,1]), c(0,1,1,1,1,1,1,1,1,1,1)) expect_equal(as.numeric(res$predictorMatrix[,2]), c(1,0,1,1,1,1,1,1,1,1,1)) expect_equal(as.numeric(res$predictorMatrix[,3]), c(1,1,0,1,1,1,1,1,1,1,1)) diff --git a/tests/testthat/test-smk-rmDS.R b/tests/testthat/test-smk-rmDS.R index aae9c5f1..0053b72c 100644 --- a/tests/testthat/test-smk-rmDS.R +++ b/tests/testthat/test-smk-rmDS.R @@ -35,10 +35,10 @@ test_that("single rmDS", { expect_equal(class(res), "list") expect_length(res, 4) - expect_equal(res$return.message, "Object(s) 'input' was deleted.", fixed = TRUE) - expect_equal(res$deleted.objects, "input", fixed = TRUE) - expect_equal(res$missing.objects, "", fixed = TRUE) - expect_equal(res$problem.objects, "", fixed = TRUE) + expect_equal(res$return.message, "Object(s) 'input' was deleted.") + expect_equal(res$deleted.objects, "input") + expect_equal(res$missing.objects, "") + expect_equal(res$problem.objects, "") }) # context("rmDS::smk::multiple") @@ -60,10 +60,10 @@ test_that("multiple rmDS", { expect_equal(class(res), "list") expect_length(res, 4) - expect_equal(res$return.message, "Object(s) 'input1,input2' was deleted.", fixed = TRUE) - expect_equal(res$deleted.objects, "input1,input2", fixed = TRUE) - expect_equal(res$missing.objects, "", fixed = TRUE) - expect_equal(res$problem.objects, "", fixed = TRUE) + expect_equal(res$return.message, "Object(s) 'input1,input2' was deleted.") + expect_equal(res$deleted.objects, "input1,input2") + expect_equal(res$missing.objects, "") + expect_equal(res$problem.objects, "") }) # context("rmDS::smk::single missing") @@ -76,10 +76,10 @@ test_that("single missing rmDS", { expect_equal(class(res), "list") expect_length(res, 4) - expect_equal(res$return.message, "Object(s) 'input' which are missing.", fixed = TRUE) - expect_equal(res$deleted.objects, "", fixed = TRUE) - expect_equal(res$missing.objects, "input", fixed = TRUE) - expect_equal(res$problem.objects, "", fixed = TRUE) + expect_equal(res$return.message, "Object(s) 'input' which are missing.") + expect_equal(res$deleted.objects, "") + expect_equal(res$missing.objects, "input") + expect_equal(res$problem.objects, "") }) @@ -95,10 +95,10 @@ test_that("multiple missing rmDS", { expect_equal(class(res), "list") expect_length(res, 4) - expect_equal(res$return.message, "Object(s) 'input1,input2' which are missing.", fixed = TRUE) - expect_equal(res$deleted.objects, "", fixed = TRUE) - expect_equal(res$missing.objects, "input1,input2", fixed = TRUE) - expect_equal(res$problem.objects, "", fixed = TRUE) + expect_equal(res$return.message, "Object(s) 'input1,input2' which are missing.") + expect_equal(res$deleted.objects, "") + expect_equal(res$missing.objects, "input1,input2") + expect_equal(res$problem.objects, "") }) # context("rmDS::smk::multiple mixed") @@ -115,10 +115,10 @@ test_that("multiple mixed rmDS", { expect_equal(class(res), "list") expect_length(res, 4) - expect_equal(res$return.message, "Object(s) 'input1' was deleted. 'input2' which are missing.", fixed = TRUE) - expect_equal(res$deleted.objects, "input1", fixed = TRUE) - expect_equal(res$missing.objects, "input2", fixed = TRUE) - expect_equal(res$problem.objects, "", fixed = TRUE) + expect_equal(res$return.message, "Object(s) 'input1' was deleted. 'input2' which are missing.") + expect_equal(res$deleted.objects, "input1") + expect_equal(res$missing.objects, "input2") + expect_equal(res$problem.objects, "") }) # diff --git a/tests/testthat/test-smk-skewnessDS1.R b/tests/testthat/test-smk-skewnessDS1.R index bfd0cceb..562c3f65 100644 --- a/tests/testthat/test-smk-skewnessDS1.R +++ b/tests/testthat/test-smk-skewnessDS1.R @@ -62,7 +62,7 @@ test_that("simple skewnessDS1, method 3", { expect_length(res, 3) expect_equal(class(res), "list") expect_equal(class(res$Skewness), "numeric") - expect_equal(res$Skewness, 0.371380, tolerance = 1e-6) + expect_equal(res$Skewness, 0.3713805, tolerance = 1e-6) expect_equal(class(res$Nvalid), "integer") expect_equal(res$Nvalid,9) expect_equal(class(res$ValidityMessage), "character") From c5ff70c2057b383304d8bd9fc4e30f3c50638d7d Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 28 Oct 2025 17:42:53 +0000 Subject: [PATCH 17/22] Updates due to 'testthat' changes --- tests/testthat/test-smk-miceDS.R | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/tests/testthat/test-smk-miceDS.R b/tests/testthat/test-smk-miceDS.R index 86df2249..3b584da5 100644 --- a/tests/testthat/test-smk-miceDS.R +++ b/tests/testthat/test-smk-miceDS.R @@ -29,15 +29,11 @@ test_that("miceDS", { ncol.pred.mat=NULL, newobj_mids='mids_object', newobj_df='impSet'), "Number of logged events: 1") expect_true(all(class(res) %in% c("list"))) - print(class(res)) expect_length(res, 3) expect_true(all(class(res$method) %in% c("character"))) - print(class(res$method)) expect_equal(as.character(res$method), c("pmm","pmm","pmm","pmm","pmm","","","","","","polyreg")) - expect_true(all(class(res$predictorMatrix) %in% c("matrix array"))) - print(class(res$predictorMatrix)) - expect_true(all(class(res$predictorMatrix) %in% c("matrix array"))) - print(class(res$predictorMatrix)) + expect_true(all(class(res$predictorMatrix) %in% c("matrix", "array"))) + expect_true(all(class(res$predictorMatrix) %in% c("matrix", "array"))) expect_equal(as.numeric(res$predictorMatrix[,1]), c(0,1,1,1,1,1,1,1,1,1,1)) expect_equal(as.numeric(res$predictorMatrix[,2]), c(1,0,1,1,1,1,1,1,1,1,1)) expect_equal(as.numeric(res$predictorMatrix[,3]), c(1,1,0,1,1,1,1,1,1,1,1)) From 004919f96c2765fc7319b37194b102a1222ffdf7 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 28 Oct 2025 21:57:29 +0000 Subject: [PATCH 18/22] Experimental dealing with 'pull_request_template' issue --- .Rbuildignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 0d7af444..77061686 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,4 +11,4 @@ ^\.circleci/config\.yml$ ^\.github$ ^cran-comments\.md$ -^pull_request_template‎$ +^pull\_request\_template‎$ From e5188a0956ef0fa1bf7cd6482ae432f4cd22a600 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 28 Oct 2025 22:55:56 +0000 Subject: [PATCH 19/22] Fix regex for pull_request_template in .Rbuildignore --- .Rbuildignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 77061686..0d7af444 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,4 +11,4 @@ ^\.circleci/config\.yml$ ^\.github$ ^cran-comments\.md$ -^pull\_request\_template‎$ +^pull_request_template‎$ From d37331a520324b11195291d42261b8f73f56a08d Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 30 Oct 2025 08:50:41 +0100 Subject: [PATCH 20/22] test: call function within correct environment --- tests/testthat/test-smk-utils.R | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test-smk-utils.R b/tests/testthat/test-smk-utils.R index 77cf9c02..517831c6 100644 --- a/tests/testthat/test-smk-utils.R +++ b/tests/testthat/test-smk-utils.R @@ -12,17 +12,20 @@ # # Set up # +.dsFunctionWrapper <- function(x) { + .loadServersideObject(x) +} # context("utils::smk::setup") test_that(".loadServersideObject() returns existing object", { test_df <- data.frame(a = 1:3) - result <- .loadServersideObject("test_df") + result <- .dsFunctionWrapper("test_df") expect_identical(result, test_df) }) test_that(".loadServersideObject() throws error for missing object", { expect_error( - .loadServersideObject("nonexistent_obj"), + .dsFunctionWrapper("test_df"), regexp = "does not exist" ) }) From 7660589cc47b83236b651dde4edf92ada8e699e3 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 30 Oct 2025 09:00:26 +0100 Subject: [PATCH 21/22] fixed pull request template in buildignore --- .Rbuildignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 0d7af444..26e4d4d4 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,4 +11,4 @@ ^\.circleci/config\.yml$ ^\.github$ ^cran-comments\.md$ -^pull_request_template‎$ +^pull_request_template$ From 4867280eca933ab69cdcb720fe9420c3cc447fc2 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Thu, 30 Oct 2025 09:11:52 +0100 Subject: [PATCH 22/22] added note explaining test setup --- tests/testthat/test-smk-utils.R | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/testthat/test-smk-utils.R b/tests/testthat/test-smk-utils.R index 517831c6..2c733cfb 100644 --- a/tests/testthat/test-smk-utils.R +++ b/tests/testthat/test-smk-utils.R @@ -12,6 +12,10 @@ # # Set up # + +## When .loadServersideObject is called, the actual data exists two levels below the function, +## i.e. data in global env --> ds function --> .loadServersideObject. We recreate this in +## the test environment with a wrapper function. .dsFunctionWrapper <- function(x) { .loadServersideObject(x) }