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$ diff --git a/DESCRIPTION b/DESCRIPTION index cf55b46a..a6737e2e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -71,10 +71,12 @@ Imports: gamlss, gamlss.dist, mice, - childsds + childsds, + glue Suggests: spelling, - testthat + testthat (>= 3.0.0) RoxygenNote: 7.3.3 Encoding: UTF-8 Language: en-GB +Config/testthat/edition: 3 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) diff --git a/R/colnamesDS.R b/R/colnamesDS.R index eb1bffb9..6dc2e99e 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 <- .loadServersideObject(x) + .checkClass(obj = x.val, obj_name = x, permitted_classes = c("data.frame", "matrix")) out <- colnames(x.val) - - # return the dimension return(out) - } #AGGREGATE FUNCTION # colnamesDS diff --git a/R/utils.R b/R/utils.R new file mode 100644 index 00000000..6fd53936 --- /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 +.loadServersideObject <- function(x) { + tryCatch( + eval(parse(text = x), envir = parent.frame(2)), + 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. +#' @importFrom glue glue glue_collapse +#' @return Invisibly returns `TRUE` if the class check passes; otherwise throws an error. +#' @noRd +.checkClass <- 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 {glue_collapse(permitted_classes, sep = ' or ')}. ", + "'{obj_name}' is type {typ}." + ) + + stop(msg, call. = FALSE) + } + + invisible(TRUE) +} 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` 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..bcbbada1 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 @@ -31,7 +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) }) @@ -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..36c4ceef 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))) @@ -42,10 +43,25 @@ 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::shutdown") -context("colnamesDS::smk::done") +# context("colnamesDS::smk::done") \ No newline at end of file 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$sums.of.squares[4], 141.06) }) -context("corDS::smk::casewise with na") +# context("corDS::smk::casewise with na") test_that("simple corDS, casewise, some", { x <- c(0.0, NA, 2.0, 3.0, NA, 5.0, NA, 7.0) y <- c(0.0, 1.0, NA, 3.0, 4.0, NA, NA, 7.0) @@ -721,6 +722,6 @@ test_that("simple corDS, casewise, some", { # Done # -context("corDS::smk::shutdown") +# context("corDS::smk::shutdown") -context("corDS::smk::done") +# context("corDS::smk::done") diff --git a/tests/testthat/test-smk-corTestDS.R b/tests/testthat/test-smk-corTestDS.R index a36e2082..b500a085 100644 --- a/tests/testthat/test-smk-corTestDS.R +++ b/tests/testthat/test-smk-corTestDS.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("corTestDS::smk::setup") +# context("corTestDS::smk::setup") # # Tests @@ -20,7 +21,7 @@ context("corTestDS::smk::setup") ########### -context("corTestDS::smk::without na, pearson") +# context("corTestDS::smk::without na, pearson") test_that("simple corTestDS, full, without na, pearson", { x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -180,7 +181,7 @@ test_that("simple corTestDS, some, pearson, without na, pearson", { expect_equal(res$`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`$data.name[[1]], "x.var and y.var") }) -context("corTestDS::smk::without na, kendall") +# context("corTestDS::smk::without na, kendall") test_that("simple corTestDS, full, without na, kendall", { x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -253,8 +254,8 @@ test_that("simple corTestDS, full, without na, kendall", { expect_equal(class(res$`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`$estimate[[1]], 1.0) @@ -345,7 +346,7 @@ test_that("simple corTestDS, some, kendall, without na, kendall", { expect_equal(class(res$`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`$estimate, 1) @@ -368,7 +369,7 @@ test_that("simple corTestDS, some, kendall, without na, kendall", { expect_equal(res$`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`$data.name[[1]], "x.var and y.var") }) -context("corTestDS::smk::without na, spearman") +# context("corTestDS::smk::without na, spearman") test_that("simple corTestDS, full, without na, spearman", { x <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) y <- c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0) @@ -439,7 +440,7 @@ test_that("simple corTestDS, full, without na, spearman", { expect_equal(class(res$`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`$estimate, 1) @@ -485,7 +486,7 @@ test_that("simple corTestDS, neg. full, without na, spearman", { expect_equal(class(res$`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`$estimate, 1) @@ -531,11 +532,11 @@ test_that("simple corTestDS, some, spearman, without na, spearman", { expect_equal(class(res$`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`$null.value, 1) @@ -554,7 +555,7 @@ test_that("simple corTestDS, some, spearman, without na, spearman", { expect_equal(res$`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..91ec685b 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) @@ -28,7 +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", { @@ -38,7 +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", { @@ -48,7 +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") }) @@ -59,7 +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", { @@ -69,7 +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", { @@ -79,13 +80,13 @@ 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") }) # # 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..3b584da5 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. @@ -12,27 +13,27 @@ # 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') 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"))) expect_length(res, 3) - expect_true("character" %in% class(res$method)) + expect_true(all(class(res$method) %in% c("character"))) 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"))) + 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)) @@ -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..0053b72c 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")) @@ -34,13 +35,13 @@ 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") +# context("rmDS::smk::multiple") test_that("multiple rmDS", { expect_false(exists("input1")) expect_false(exists("input2")) @@ -59,13 +60,13 @@ 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") +# context("rmDS::smk::single missing") test_that("single missing rmDS", { expect_false(exists("input")) @@ -75,14 +76,14 @@ 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, "") }) -context("rmDS::smk::multiple missing") +# context("rmDS::smk::multiple missing") test_that("multiple missing rmDS", { expect_false(exists("input1")) expect_false(exists("input2")) @@ -94,13 +95,13 @@ 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") +# context("rmDS::smk::multiple mixed") test_that("multiple mixed rmDS", { expect_false(exists("input1")) expect_false(exists("input2")) @@ -114,16 +115,16 @@ 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, "") }) # # 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..562c3f65 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) @@ -61,7 +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") @@ -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-utils.R b/tests/testthat/test-smk-utils.R new file mode 100644 index 00000000..2c733cfb --- /dev/null +++ b/tests/testthat/test-smk-utils.R @@ -0,0 +1,53 @@ + +#------------------------------------------------------------------------------- +# 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 +# + +## 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) +} + +# context("utils::smk::setup") +test_that(".loadServersideObject() returns existing object", { + test_df <- data.frame(a = 1:3) + result <- .dsFunctionWrapper("test_df") + expect_identical(result, test_df) +}) + +test_that(".loadServersideObject() throws error for missing object", { + expect_error( + .dsFunctionWrapper("test_df"), + 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") 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")