diff --git a/.Rbuildignore b/.Rbuildignore index e05151613..b66ab8982 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,8 +17,8 @@ ^R/secure.global.ranking.md$ ^_pkgdown\.yml$ ^docs$ -^dsBase_6.3.4.tar.gz$ -^dsBase_6.3.4-permissive.tar.gz$ +^dsBase_6.3.5.tar.gz$ +^dsBase_6.3.5-permissive.tar.gz$ ^dsDanger_6.3.4.tar.gz$ ^\.circleci$ ^\.circleci/config\.yml$ diff --git a/DESCRIPTION b/DESCRIPTION index cc110b7f7..f87cb256d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: dsBaseClient Title: 'DataSHIELD' Client Side Base Functions -Version: 6.3.4 +Version: 6.3.5-9000 Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have been designed to only share non disclosive summary statistics, with built in automated output diff --git a/README.md b/README.md index c82341b5f..616c30dcd 100644 --- a/README.md +++ b/README.md @@ -23,8 +23,8 @@ And the development version from install.packages("remotes") remotes::install_github("datashield/dsBaseClient", "") -# Install v6.3.4 with the following -remotes::install_github("datashield/dsBaseClient", "6.3.4") +# Install v6.3.5 with the following +remotes::install_github("datashield/dsBaseClient", "6.3.5") ``` For a full list of development branches, checkout https://github.com/datashield/dsBaseClient/branches @@ -50,7 +50,7 @@ The code here is organised as: [1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà Montagut X, Wheater S (2025). - _dsBaseClient: 'DataSHIELD' Client Side Base Functions_. R package version 6.3.4. + _dsBaseClient: 'DataSHIELD' Client Side Base Functions_. R package version 6.3.5. [2] Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 8439c8cef..b7f98439e 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.4-dev + displayName: Nightly build - v6.3.5-dev branches: include: - - v6.3.4-dev + - v6.3.5-dev always: true ######################################################################################### @@ -235,7 +235,7 @@ jobs: curl -u admin:admin -X GET http://localhost:8080/packages - curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package sleep 60 docker container restart dsbaseclient_armadillo_1 diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 37bb6c775..db3d7a186 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -44,10 +44,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.4-dev + displayName: Nightly build - v6.3.5-dev branches: include: - - v6.3.4-dev + - v6.3.5-dev always: true ######################################################################################### @@ -216,7 +216,7 @@ jobs: - bash: | R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.4-dev'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)" sleep 60 diff --git a/dsBase_6.3.4.tar.gz b/dsBase_6.3.5-permissive.tar.gz similarity index 57% rename from dsBase_6.3.4.tar.gz rename to dsBase_6.3.5-permissive.tar.gz index c7725adf9..3703315dd 100644 Binary files a/dsBase_6.3.4.tar.gz and b/dsBase_6.3.5-permissive.tar.gz differ diff --git a/dsBase_6.3.4-permissive.tar.gz b/dsBase_6.3.5.tar.gz similarity index 51% rename from dsBase_6.3.4-permissive.tar.gz rename to dsBase_6.3.5.tar.gz index c7c2f2b24..0ea538d0f 100644 Binary files a/dsBase_6.3.4-permissive.tar.gz and b/dsBase_6.3.5.tar.gz differ diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index 6c6103d4a..dab96a79e 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.4-dev + displayName: Nightly build - v6.3.5-dev branches: include: - - v6.3.4-dev + - v6.3.5-dev always: true ######################################################################################### @@ -235,7 +235,7 @@ jobs: - bash: | R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.4-dev'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)" sleep 60 diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index 4c55c6e74..512e649c1 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -8,11 +8,12 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see . #------------------------------------------------------------------------------- + # # Datashield test suite set up # -context("setup - start") +# context("setup - start") # Convert 'warnings' to 'errors' # options(warn = 2) @@ -33,4 +34,4 @@ source("connection_to_datasets/init_studies_datasets.R") source("connection_to_datasets/init_discordant_datasets.R") source("connection_to_datasets/init_mediation_datasets.R") -context("setup - done") +# context("setup - done") diff --git a/tests/testthat/teardown.R b/tests/testthat/teardown.R index 710dac810..5026a0dbf 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") +# context("teardown") -context("teardown - done") +# context("teardown - done") diff --git a/tests/testthat/test-_-vm-test.R b/tests/testthat/test-_-vm-test.R index 952425f56..7b5af1f4e 100644 --- a/tests/testthat/test-_-vm-test.R +++ b/tests/testthat/test-_-vm-test.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("vm-test::_::setup") +# context("vm-test::_::setup") init.testing.datasets() @@ -21,7 +22,7 @@ init.testing.datasets() # #connect to a server -context("vm-test::_::tests::vm") +# context("vm-test::_::tests::vm") test_that("The virtual machine is loaded. ", { @@ -33,11 +34,11 @@ test_that("The virtual machine is loaded. ", # Shutdown # -context("vm-test::_::shutdown") +# context("vm-test::_::shutdown") # # Done # -context("vm-test::_::done") +# context("vm-test::_::done") diff --git a/tests/testthat/test-arg-ds.Boole.R b/tests/testthat/test-arg-ds.Boole.R index fdfc45026..d8fb3bedf 100644 --- a/tests/testthat/test-arg-ds.Boole.R +++ b/tests/testthat/test-arg-ds.Boole.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.Boole::arg::test errors") +# context("ds.Boole::arg::test errors") test_that("Boole_erros", { expect_error(ds.Boole(), "Please provide the name of the column or scalar that holds V1!", fixed=TRUE) expect_error(ds.Boole(V1="D$LAB_TSC"), "Please provide the name of a column or scalar holding V2 or declare a scalar in character format: eg '3'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.asCharacter.R b/tests/testthat/test-arg-ds.asCharacter.R index a007ec6a3..8d7d35449 100644 --- a/tests/testthat/test-arg-ds.asCharacter.R +++ b/tests/testthat/test-arg-ds.asCharacter.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. @@ -18,7 +19,7 @@ connect.discordant.dataset.simple(list("A", "B", "C")) # Tests # -context("ds.asCharacter::arg::test errors") +# context("ds.asCharacter::arg::test errors") test_that("asCharacter_erros", { expect_error(ds.asCharacter(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asDataMatrix.R b/tests/testthat/test-arg-ds.asDataMatrix.R index e84e2281b..ca65f6cb0 100644 --- a/tests/testthat/test-arg-ds.asDataMatrix.R +++ b/tests/testthat/test-arg-ds.asDataMatrix.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asDataMatrix::arg::test errors") +# context("ds.asDataMatrix::arg::test errors") test_that("asDataMatrix_erros", { expect_error(ds.asDataMatrix(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asFactor.R b/tests/testthat/test-arg-ds.asFactor.R index bfc4662dc..a264b040a 100644 --- a/tests/testthat/test-arg-ds.asFactor.R +++ b/tests/testthat/test-arg-ds.asFactor.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asFactor::arg::test errors") +# context("ds.asFactor::arg::test errors") test_that("asFactor_erros", { expect_error(ds.asFactor(), "Please provide the name of the variable that is to be converted to a factor e.g. 'varname'", fixed=TRUE) expect_error(ds.asFactor(input.var.name=1), "Please provide the name of the variable that is to be converted to a factor in character format e.g. 'varname'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.asInteger.R b/tests/testthat/test-arg-ds.asInteger.R index a6a1196ef..c6305012e 100644 --- a/tests/testthat/test-arg-ds.asInteger.R +++ b/tests/testthat/test-arg-ds.asInteger.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asInteger::arg::test errors") +# context("ds.asInteger::arg::test errors") test_that("asInteger_erros", { expect_error(ds.asInteger(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asList.R b/tests/testthat/test-arg-ds.asList.R index c498d36cd..926401881 100644 --- a/tests/testthat/test-arg-ds.asList.R +++ b/tests/testthat/test-arg-ds.asList.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asList::arg::test errors") +# context("ds.asList::arg::test errors") test_that("asList_erros", { expect_error(ds.asList(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asLogical.R b/tests/testthat/test-arg-ds.asLogical.R index 64912059a..39056cc38 100644 --- a/tests/testthat/test-arg-ds.asLogical.R +++ b/tests/testthat/test-arg-ds.asLogical.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asLogical::arg::test errors") +# context("ds.asLogical::arg::test errors") test_that("asLogical_erros", { expect_error(ds.asLogical(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asMatrix.R b/tests/testthat/test-arg-ds.asMatrix.R index 5c7c8ebdf..4a199dd08 100644 --- a/tests/testthat/test-arg-ds.asMatrix.R +++ b/tests/testthat/test-arg-ds.asMatrix.R @@ -1,4 +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. @@ -17,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asMatrix::arg::test errors") +# context("ds.asMatrix::arg::test errors") test_that("asMatrix_erros", { expect_error(ds.asMatrix(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.asNumeric.R b/tests/testthat/test-arg-ds.asNumeric.R index b821c8429..276260751 100644 --- a/tests/testthat/test-arg-ds.asNumeric.R +++ b/tests/testthat/test-arg-ds.asNumeric.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.asNumeric::arg::test errors") +# context("ds.asNumeric::arg::test errors") test_that("asNumeric_erros", { expect_error(ds.asNumeric(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.assign.R b/tests/testthat/test-arg-ds.assign.R index 9c1cdac01..4fbd06c42 100644 --- a/tests/testthat/test-arg-ds.assign.R +++ b/tests/testthat/test-arg-ds.assign.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.assign::arg::test errors") +# context("ds.assign::arg::test errors") test_that("assign_erros", { expect_error(ds.assign(), "Please give the name of object to assign or an expression to evaluate and assign.!\n") }) diff --git a/tests/testthat/test-arg-ds.auc.R b/tests/testthat/test-arg-ds.auc.R index 7c42585f3..ade352110 100644 --- a/tests/testthat/test-arg-ds.auc.R +++ b/tests/testthat/test-arg-ds.auc.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. @@ -12,13 +13,13 @@ # Set up # -context("ds.auc::arg::setup") +# context("ds.auc::arg::setup") # # Tests # -context("ds.auc::arg::test errors") +# context("ds.auc::arg::test errors") test_that("ds.auc errors for null pred or y", { @@ -31,5 +32,5 @@ test_that("ds.auc errors for null pred or y", { # Done # -context("ds.auc::arg::shutdown") -context("ds.auc::arg::done") +# context("ds.auc::arg::shutdown") +# context("ds.auc::arg::done") diff --git a/tests/testthat/test-arg-ds.c.R b/tests/testthat/test-arg-ds.c.R index 3371d591d..7a85cecb4 100644 --- a/tests/testthat/test-arg-ds.c.R +++ b/tests/testthat/test-arg-ds.c.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.c::arg::test errors") +# context("ds.c::arg::test errors") test_that("simple c errors", { expect_error(ds.c(), "x=NULL. Please provide the names of the objects to concatenate!") }) diff --git a/tests/testthat/test-arg-ds.cbind.R b/tests/testthat/test-arg-ds.cbind.R index d600ac830..a51988136 100644 --- a/tests/testthat/test-arg-ds.cbind.R +++ b/tests/testthat/test-arg-ds.cbind.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.cbind::arg::test errors") +# context("ds.cbind::arg::test errors") test_that("cbind_erros", { ds.asList(x='D$LAB_TSC', newobj="as_list") diff --git a/tests/testthat/test-arg-ds.changeRefGroup.R b/tests/testthat/test-arg-ds.changeRefGroup.R index 1baffe404..91a0fe24c 100644 --- a/tests/testthat/test-arg-ds.changeRefGroup.R +++ b/tests/testthat/test-arg-ds.changeRefGroup.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("DIS_AMI", "LAB_TSC")) # Tests # -context("ds.changeRefGroup::arg::test errors") +# context("ds.changeRefGroup::arg::test errors") test_that("changeRefGroup_erros", { expect_error(ds.changeRefGroup(), "Please provide the name of a vector of type factor!") expect_error(ds.changeRefGroup(x="D$DIS_AMI"), " You must indicate a reference level - set the parameter 'ref'.") diff --git a/tests/testthat/test-arg-ds.class.R b/tests/testthat/test-arg-ds.class.R index c7240c7b0..c0bf5c7dd 100644 --- a/tests/testthat/test-arg-ds.class.R +++ b/tests/testthat/test-arg-ds.class.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.class::arg::test errors") +# context("ds.class::arg::test errors") test_that("class_erros", { expect_error(ds.class(), "Please provide the name of the input object!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.colnames.R b/tests/testthat/test-arg-ds.colnames.R index bbbaa5e97..39ce9b87a 100644 --- a/tests/testthat/test-arg-ds.colnames.R +++ b/tests/testthat/test-arg-ds.colnames.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.colnames::arg::test errors") +# context("ds.colnames::arg::test errors") test_that("simple colnames errors", { expect_error(ds.colnames(), "") }) diff --git a/tests/testthat/test-arg-ds.completeCases.R b/tests/testthat/test-arg-ds.completeCases.R index a13856380..8bb997338 100644 --- a/tests/testthat/test-arg-ds.completeCases.R +++ b/tests/testthat/test-arg-ds.completeCases.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.completeCases::arg::test errors") +# context("ds.completeCases::arg::test errors") test_that("completeCases_errors", { res <- ds.completeCases() expect_equal(res, "Error: x1 must be a character string naming a serverside data.frame, matrix or vector", fixed = TRUE) diff --git a/tests/testthat/test-arg-ds.cor.R b/tests/testthat/test-arg-ds.cor.R index 9f728e1a0..47b5a5abb 100644 --- a/tests/testthat/test-arg-ds.cor.R +++ b/tests/testthat/test-arg-ds.cor.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.cor::arg::test errors") +# context("ds.cor::arg::test errors") test_that("cor_erros", { expect_error(ds.cor(), 'x=NULL. Please provide the name of a matrix or dataframe or the names of two numeric vectors!', fixed=TRUE) expect_error(ds.cor(x='D$LAB_TSC'), 'If x is a numeric vector, y must be a numeric vector!', fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.corTest.R b/tests/testthat/test-arg-ds.corTest.R index ac80a40cc..76adc6f15 100644 --- a/tests/testthat/test-arg-ds.corTest.R +++ b/tests/testthat/test-arg-ds.corTest.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. @@ -18,7 +19,7 @@ connect.studies.dataset.survival(list("survtime", "time.id")) # Tests # -context("ds.corTest::arg") +# context("ds.corTest::arg") test_that("simple arg test", { expect_error(ds.corTest(), "x=NULL. Please provide the names of the 1st numeric vector!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.cov.R b/tests/testthat/test-arg-ds.cov.R index 0958c65ad..29330c9de 100644 --- a/tests/testthat/test-arg-ds.cov.R +++ b/tests/testthat/test-arg-ds.cov.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.cov::arg::test errors") +# context("ds.cov::arg::test errors") test_that("cov_erros", { expect_error(ds.cov(), 'x=NULL. Please provide the name of a matrix or dataframe or the names of two numeric vectors!', fixed=TRUE) expect_error(ds.cov(x='D$LAB_TSC'), 'If x is a numeric vector, y must be a numeric vector!', fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.dataFrame.R b/tests/testthat/test-arg-ds.dataFrame.R index 9d76b7beb..33fa65cf6 100644 --- a/tests/testthat/test-arg-ds.dataFrame.R +++ b/tests/testthat/test-arg-ds.dataFrame.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.dataFrame::arg::test errors") +# context("ds.dataFrame::arg::test errors") test_that("dataframe_erros", { expect_error(ds.dataFrame(), "Please provide the name of the list that holds the input vectors!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.dataFrameFill.R b/tests/testthat/test-arg-ds.dataFrameFill.R index 0e71d2e56..2eb77e4f1 100644 --- a/tests/testthat/test-arg-ds.dataFrameFill.R +++ b/tests/testthat/test-arg-ds.dataFrameFill.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.dataFrameFill::arg::test errors") +# context("ds.dataFrameFill::arg::test errors") test_that("dataFrameFill_erros", { expect_error(ds.dataFrameFill(), "Please provide the name of the data.frame to be filled as a character string: eg 'xxx'", fixed=TRUE) expect_error(ds.dataFrameFill("NonDF"), "The input object NonDF is not defined in sim1, sim2, sim3!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.dataFrameSort.R b/tests/testthat/test-arg-ds.dataFrameSort.R index 65a1c2cfe..52061313f 100644 --- a/tests/testthat/test-arg-ds.dataFrameSort.R +++ b/tests/testthat/test-arg-ds.dataFrameSort.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) # Tests # -context("ds.dataFrameSort::arg::no args") +# context("ds.dataFrameSort::arg::no args") test_that("dataFrameSort_noargs", { expect_error(ds.dataFrameSort(), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -30,7 +31,7 @@ test_that("dataFrameSort_noargs", { expect_match(res.errors$sim3, "* Error in strsplit\\(df.name, split = \"\"\\) : non-character argument*") }) -context("ds.dataFrameSort::arg::sorted dataframe, of factors") +# context("ds.dataFrameSort::arg::sorted dataframe, of factors") test_that("dataFrameSort_factors", { myvectors <- c('D$LAB_TSC', 'D$GENDER') ds.dataFrame(x=myvectors, newobj="unsorted_df") diff --git a/tests/testthat/test-arg-ds.dataFrameSubset.R b/tests/testthat/test-arg-ds.dataFrameSubset.R index 4bd414e6e..53ec07e39 100644 --- a/tests/testthat/test-arg-ds.dataFrameSubset.R +++ b/tests/testthat/test-arg-ds.dataFrameSubset.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # 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. @@ -13,7 +14,7 @@ # Set up # -context("ds.dataFrameSubset::arg::setup") +# context("ds.dataFrameSubset::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -25,27 +26,27 @@ test_that("setup", { # Tests # -context("ds.dataFrameSubset::arg::missing 'ds.name' arg errors") +# context("ds.dataFrameSubset::arg::missing 'ds.name' arg errors") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(), "Please provide the name of the data.frame to be subsetted as a character string: eg 'xxx'", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'V1' arg error") +# context("ds.dataFrameSubset::arg::missing 'V1' arg error") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D"), "Please provide the name of the column or scalar that holds V1 as a character string: eg 'xxx' or '3'", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'V2' arg error") +# context("ds.dataFrameSubset::arg::missing 'V2' arg error") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="LAB_TSC"), "Please provide the name of the column or scalar that holds V2 as a character string: eg 'xxx' or '3'", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'Boolean.operator' arg error") +# context("ds.dataFrameSubset::arg::missing 'Boolean.operator' arg error") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="LAB_TSC", V2.name="LAB_TSC"), "Unless you are only subsetting columns, please provide a Boolean operator in character format: eg '==' or '>=' or '<' or '!='. However, if either keep.cols or rm.cols is non-null because you want to subset columns and you specify both V1.name and V2.name as NULL (or 'ONES') and Boolean.operator as NULL,ds.dataFrameSubset will subset out the specified columns but will keep all rows.", fixed=TRUE) }) -context("ds.dataFrameSubset::arg::missing 'df.name' value server-side") +# context("ds.dataFrameSubset::arg::missing 'df.name' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="M", V1.name="A", V2.name="B", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -57,7 +58,7 @@ test_that("dataFrameSubset_erros", { expect_match(res.errors$sim3, "* object 'M' not found*") }) -context("ds.dataFrameSubset::arg::missing 'V1' value server-side") +# context("ds.dataFrameSubset::arg::missing 'V1' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="A", V2.name="B", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -69,7 +70,7 @@ test_that("dataFrameSubset_erros", { expect_match(res.errors$sim3, "* Error in eval\\(parse\\(text = V1.name\\), envir = parent.frame\\(\\)\\) : \\n object 'A' not found*") }) -context("ds.dataFrameSubset::arg::missing 'V2' value server-side") +# context("ds.dataFrameSubset::arg::missing 'V2' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="D$LAB_TSC", V2.name="B", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -81,7 +82,7 @@ test_that("dataFrameSubset_erros", { expect_match(res.errors$sim3, "* Error in eval\\(parse\\(text = V2.name\\), envir = parent.frame\\(\\)\\) : \\n object 'B' not found*") }) -context("ds.dataFrameSubset::arg::invalid 'Boolean.operator' value server-side") +# context("ds.dataFrameSubset::arg::invalid 'Boolean.operator' value server-side") test_that("dataFrameSubset_erros", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="D$LAB_TSC", V2.name="D$LAB_TSC", Boolean.operator="=/="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) @@ -97,7 +98,7 @@ test_that("dataFrameSubset_erros", { # Shutdown # -context("ds.dataFrameSubset::arg::shutdown") +# context("ds.dataFrameSubset::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -109,4 +110,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.dataFrameSubset::arg::done") +# context("ds.dataFrameSubset::arg::done") diff --git a/tests/testthat/test-arg-ds.dim.R b/tests/testthat/test-arg-ds.dim.R index 8ee681985..27b4e8bd8 100644 --- a/tests/testthat/test-arg-ds.dim.R +++ b/tests/testthat/test-arg-ds.dim.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.dim::arg::test errors") +# context("ds.dim::arg::test errors") test_that("dim_erros", { expect_error(ds.dim(), "Please provide the name of a data.frame or matrix!", fixed=TRUE) expect_error(ds.dim(x="F", checks = TRUE), "The input object must be a table structure!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.exists.R b/tests/testthat/test-arg-ds.exists.R index 7e920395f..8ae2070d3 100644 --- a/tests/testthat/test-arg-ds.exists.R +++ b/tests/testthat/test-arg-ds.exists.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.exists::arg::test errors") +# context("ds.exists::arg::test errors") test_that("simple exists errors", { expect_error(ds.exists(), "Please provide the name of the input object!") }) diff --git a/tests/testthat/test-arg-ds.exp.R b/tests/testthat/test-arg-ds.exp.R index d3a6d1ef9..c851bba34 100644 --- a/tests/testthat/test-arg-ds.exp.R +++ b/tests/testthat/test-arg-ds.exp.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.exp::arg::test errors") +# context("ds.exp::arg::test errors") test_that("exp_erros", { expect_error(ds.exp(), "Please provide the name of the input object!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.foobar.R b/tests/testthat/test-arg-ds.foobar.R index 05cbde701..36d5ac977 100644 --- a/tests/testthat/test-arg-ds.foobar.R +++ b/tests/testthat/test-arg-ds.foobar.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("ds.foobar::arg::setup") +# context("ds.foobar::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.foobar::arg::aggregate") +# context("ds.foobar::arg::aggregate") test_that("NULL connections", { calltext <- call("fooBarDS") if (ds.test_env$driver == "ArmadilloDriver") { @@ -40,7 +41,7 @@ test_that("NULL connections", { expect_length(errs, 0) }) -context("ds.foobar::arg::aggregate") +# context("ds.foobar::arg::aggregate") test_that("NULL expr", { calltext <- call("fooBarDS") expect_error(expect_warning(datashield.aggregate(conns=ds.test_env$connections, expr=NULL), "'x' is NULL so the result will be NULL", fixed = TRUE), "replacement has length zero", fixed = TRUE) @@ -49,7 +50,7 @@ test_that("NULL expr", { expect_length(errs, 0) }) -context("ds.foobar::arg::aggregate") +# context("ds.foobar::arg::aggregate") test_that("non existent aggregate foobarDS", { calltext <- call("fooBarDS") expect_error(datashield.aggregate(conns=ds.test_env$connections, expr=calltext)) @@ -65,7 +66,7 @@ test_that("non existent aggregate foobarDS", { expect_true(errs$sim3 %in% c("Command 'fooBarDS()' failed on 'sim3': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: No such DataSHIELD 'AGGREGATE' method with name: fooBarDS")) }) -context("ds.foobar::arg::assign") +# context("ds.foobar::arg::assign") test_that("NULL connections", { calltext <- call("fooBarDS") if (ds.test_env$driver == "ArmadilloDriver") { @@ -89,7 +90,7 @@ test_that("NULL connections", { # expect_length(res, 0) #}) -context("ds.foobar::arg::assign") +# context("ds.foobar::arg::assign") test_that("NULL value", { calltext <- call("fooBarDS") expect_error(datashield.assign(conns=ds.test_env$connections, symbol="new_obj", value=NULL), "Not a valid table name", fixed=TRUE) @@ -98,7 +99,7 @@ test_that("NULL value", { expect_length(errs, 0) }) -context("ds.foobar::arg::assign") +# context("ds.foobar::arg::assign") test_that("non existent assign foobarDS", { calltext <- call("fooBarDS") expect_error(datashield.assign(conns=ds.test_env$connections, symbol="new_obj", value=calltext)) @@ -117,7 +118,7 @@ test_that("non existent assign foobarDS", { # Tear down # -context("ds.foobar::arg::shutdown") +# context("ds.foobar::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -125,4 +126,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.foobar::arg::done") +# context("ds.foobar::arg::done") diff --git a/tests/testthat/test-arg-ds.gamlss.R b/tests/testthat/test-arg-ds.gamlss.R index 7a4ec4737..c24f41efb 100644 --- a/tests/testthat/test-arg-ds.gamlss.R +++ b/tests/testthat/test-arg-ds.gamlss.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. @@ -18,7 +19,7 @@ connect.studies.dataset.gamlss(list("e3_bw", "e3_gac_None")) # Tests # -context("ds.gamlss::arg::test errors") +# context("ds.gamlss::arg::test errors") test_that("gamlss_errors", { expect_error(ds.gamlss(), " Please provide a valid formula!", fixed=TRUE) expect_error(ds.gamlss(formula="e3_bw ~ e3_gac_None", method="RG"), "Argument 'method' must be either 'RS', 'CG' or 'mixed'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.glm.R b/tests/testthat/test-arg-ds.glm.R index 0724e206b..fbf1a880f 100644 --- a/tests/testthat/test-arg-ds.glm.R +++ b/tests/testthat/test-arg-ds.glm.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.glm::arg::test errors") +# context("ds.glm::arg::test errors") test_that("glm_errors", { expect_error(ds.glm(), " Please provide a valid regression formula!", fixed=TRUE) expect_error(ds.glm("D$LAB_TSC~D$LAB_TSC"), " Please provide a valid 'family' argument!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.glmPredict.R b/tests/testthat/test-arg-ds.glmPredict.R index 579fa5b54..52c70b5c1 100644 --- a/tests/testthat/test-arg-ds.glmPredict.R +++ b/tests/testthat/test-arg-ds.glmPredict.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,14 +19,14 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", # Tests # -context("ds.glmPredict::arg::test _glmname_ arg is correct object") +# context("ds.glmPredict::arg::test _glmname_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict(), " is not set, please specify it as a character string containing the name of a valid glm class object on the serverside", fixed=TRUE) expect_error(ds.glmPredict("ABC"), "The input object ABC is not defined in sim1, sim2, sim3!", fixed=TRUE) }) -context("ds.glmPredict::arg::setting up glm obj for further testing") +# context("ds.glmPredict::arg::setting up glm obj for further testing") test_that("glmPredict_errors", { #glm.obj <- ds.glmSLMA('D$LAB_TSC~D$LAB_TSC', family="gaussian", newobj="gaussian.glmslma.obj") #glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -37,7 +38,7 @@ test_that("glmPredict_errors", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmPredict::arg::test _newdataname_ arg is correct object") +# context("ds.glmPredict::arg::test _newdataname_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = "help"),"There are some DataSHIELD errors, list them with datashield.errors()", fixed=TRUE) # TODO: "some DataSHIELD errors" is unhelpful and needs improvement @@ -46,13 +47,13 @@ test_that("glmPredict_errors", { expect_true(all(c("sim1","sim2","sim3") %in% names(datashield.errors()))) }) -context("ds.glmPredict::arg::test _output.type_ arg is correct object") +# context("ds.glmPredict::arg::test _output.type_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = NULL), "missing value where TRUE/FALSE needed", fixed=TRUE) expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = 'blah'), " is not correctly set, please specify it as one of three character strings: 'link', 'response', or 'terms'", fixed=TRUE) }) -context("ds.glmPredict::arg::test _se.fit_ arg is correct object") +# context("ds.glmPredict::arg::test _se.fit_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "response", se.fit = "1"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -66,12 +67,12 @@ test_that("glmPredict_errors", { # res <- ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "response", se.fit = FALSE, dispersion = "thereisnothingontheservercalledthis") #}) -context("ds.glmPredict::arg::test _terms_ arg is correct object") +# context("ds.glmPredict::arg::test _terms_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "terms", se.fit = FALSE, dispersion = NULL, terms="thereisnothingontheservercalledthis2"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) }) -context("ds.glmPredict::arg::test _na.action_ arg is correct object") +# context("ds.glmPredict::arg::test _na.action_ arg is correct object") test_that("glmPredict_errors", { expect_error(ds.glmPredict("gaussian.glmslma.obj", newdataname = NULL, output.type = "response", se.fit = FALSE, dispersion = NULL, terms=NULL, na.action= "na.other"), " is not correctly set, please specify it as one of four character strings: 'na.fail', 'na.omit', 'na.exclude' or 'na.pass'", fixed = TRUE) }) diff --git a/tests/testthat/test-arg-ds.glmSLMA.R b/tests/testthat/test-arg-ds.glmSLMA.R index ce4dbe735..4180f91af 100644 --- a/tests/testthat/test-arg-ds.glmSLMA.R +++ b/tests/testthat/test-arg-ds.glmSLMA.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.glmSLMA::arg::test errors") +# context("ds.glmSLMA::arg::test errors") test_that("glmSLMA_errors", { expect_error(ds.glmSLMA(), " Please provide a valid regression formula!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.glmerSLMA.R b/tests/testthat/test-arg-ds.glmerSLMA.R index 84662f7f2..36c80bb5b 100644 --- a/tests/testthat/test-arg-ds.glmerSLMA.R +++ b/tests/testthat/test-arg-ds.glmerSLMA.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("ds.glmerSLMA::arg::setup") +# context("ds.glmerSLMA::arg::setup") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Test # -context("ds.glmerSLMA::arg::testing") +# context("ds.glmerSLMA::arg::testing") test_that("simple glmerSLMA tesing (mis)use of arguments", { expect_error(ds.glmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D'), " Please provide a valid 'family' argument!", fixed=TRUE) @@ -53,7 +54,7 @@ test_that("simple glmerSLMA tesing (mis)use of arguments", { # Shutdown # -context("ds.glmerSLMA::arg::shutdown") +# context("ds.glmerSLMA::arg::shutdown") test_that("setup", { ds_expect_variables(c("D", "offset", "weights")) @@ -65,4 +66,4 @@ disconnect.studies.dataset.cluster.int() # Done # -context("ds.glmerSLMA::arg::done") +# context("ds.glmerSLMA::arg::done") diff --git a/tests/testthat/test-arg-ds.isNA.R b/tests/testthat/test-arg-ds.isNA.R index 27c9bffcb..433857a75 100644 --- a/tests/testthat/test-arg-ds.isNA.R +++ b/tests/testthat/test-arg-ds.isNA.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_HDL")) # Tests # -context("ds.isNA::arg::errors") +# context("ds.isNA::arg::errors") test_that("isNA errors", { expect_error(ds.isNA(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.isValid.R b/tests/testthat/test-arg-ds.isValid.R index 65d843cc7..37fbf21a5 100644 --- a/tests/testthat/test-arg-ds.isValid.R +++ b/tests/testthat/test-arg-ds.isValid.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_HDL")) # Tests # -context("ds.isValid::arg::errors") +# context("ds.isValid::arg::errors") test_that("isValid errors", { expect_error(ds.isValid(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.isValid("D$NOT_THERE"), "The input object D$NOT_THERE is not defined in sim1, sim2, sim3!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.kurtosis.R b/tests/testthat/test-arg-ds.kurtosis.R index db80a0788..0d8118e12 100644 --- a/tests/testthat/test-arg-ds.kurtosis.R +++ b/tests/testthat/test-arg-ds.kurtosis.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.kurtosis::arg::setup") +# context("ds.kurtosis::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.kurtosis::arg::test errors") +# context("ds.kurtosis::arg::test errors") test_that("kurtosis_erros", { expect_error(ds.kurtosis(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.kurtosis(x='D$LAB_TSC', type='datashield'), "Function argument \"type\" has to be either \"both\", \"combine\" or \"split\"", fixed=TRUE) @@ -36,7 +37,7 @@ test_that("kurtosis_erros", { # Done # -context("ds.kurtosis::arg::shutdown") +# context("ds.kurtosis::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,4 +45,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.kurtosis::arg::done") +# context("ds.kurtosis::arg::done") diff --git a/tests/testthat/test-arg-ds.length.R b/tests/testthat/test-arg-ds.length.R index 87d5f3b3c..06ce3a7a5 100644 --- a/tests/testthat/test-arg-ds.length.R +++ b/tests/testthat/test-arg-ds.length.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.length::arg::test errors") +# context("ds.length::arg::test errors") test_that("length_erros", { ds.asMatrix(x='D$LAB_TSC', newobj="not_a_numeric") diff --git a/tests/testthat/test-arg-ds.levels.R b/tests/testthat/test-arg-ds.levels.R index 6f94c4ec9..cf6bf974b 100644 --- a/tests/testthat/test-arg-ds.levels.R +++ b/tests/testthat/test-arg-ds.levels.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.levels::arg") +# context("ds.levels::arg") test_that("simple levels", { expect_error(ds.levels(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.levels("LAB_TSC"), "The input object LAB_TSC is not defined in sim1, sim2, sim3!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.lexis.R b/tests/testthat/test-arg-ds.lexis.R index 681598e07..52d1657df 100644 --- a/tests/testthat/test-arg-ds.lexis.R +++ b/tests/testthat/test-arg-ds.lexis.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -19,12 +19,12 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.lexis::arg::test errors") +# context("ds.lexis::arg::test errors") test_that("lexis_erros", { expect_error(ds.lexis(), "Please provide the name of the column that holds the subject IDs!", fixed=TRUE) }) -context("ds.lexis::arg::test intervalWidth") +# context("ds.lexis::arg::test intervalWidth") test_that("simple lexis", { expect_error(ds.lexis(data='D', intervalWidth = NA, idCol = 'D$id', entryCol = 'D$starttime', exitCol = 'D$endtime', statusCol = 'D$cens', variables = c('D$age.60'), expandDF = 'EM.new'), "Please provide a (non-zero) single numeric value or vector to identify the survival time intervals", fixed = TRUE) expect_error(ds.lexis(data='D', intervalWidth = NULL, idCol = 'D$id', entryCol = 'D$starttime', exitCol = 'D$endtime', statusCol = 'D$cens', variables = c('D$age.60'), expandDF = 'EM.new'), "Please provide a (non-zero) single numeric value or vector to identify the survival time intervals", fixed = TRUE) diff --git a/tests/testthat/test-arg-ds.list.R b/tests/testthat/test-arg-ds.list.R index ffbcb7496..b2bc229d6 100644 --- a/tests/testthat/test-arg-ds.list.R +++ b/tests/testthat/test-arg-ds.list.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.list::arg::test errors") +# context("ds.list::arg::test errors") test_that("simple ds.list errors", { expect_error(ds.list(), "x=NULL. Please provide the names of the objects to coerce into a list!") }) diff --git a/tests/testthat/test-arg-ds.lmerSLMA.R b/tests/testthat/test-arg-ds.lmerSLMA.R index bd229260b..d5f6510da 100644 --- a/tests/testthat/test-arg-ds.lmerSLMA.R +++ b/tests/testthat/test-arg-ds.lmerSLMA.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("ds.lmerSLMA::arg::setup") +# context("ds.lmerSLMA::arg::setup") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::arg") +# context("ds.lmerSLMA::arg") test_that("simple lmerSLMA tesing (mis)use of arguments", { res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male', dataName = 'D') expect_equal(res$study1$errorMessage, "No random effects terms specified in formula", fixed=TRUE) @@ -50,7 +51,7 @@ test_that("simple lmerSLMA tesing (mis)use of arguments", { # Shutdown # -context("ds.lmerSLMA::arg::shutdown") +# context("ds.lmerSLMA::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "offset", "offset.to.use", "weights", "weights.to.use")) @@ -62,4 +63,4 @@ disconnect.studies.dataset.cluster.int() # Done # -context("ds.lmerSLMA::arg::done") +# context("ds.lmerSLMA::arg::done") diff --git a/tests/testthat/test-arg-ds.log.R b/tests/testthat/test-arg-ds.log.R index d2510c08f..b51cdf7d4 100644 --- a/tests/testthat/test-arg-ds.log.R +++ b/tests/testthat/test-arg-ds.log.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.log::arg::test errors") +# context("ds.log::arg::test errors") test_that("log_erros", { expect_error(ds.log(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.look.R b/tests/testthat/test-arg-ds.look.R index f1d7e6951..705660be7 100644 --- a/tests/testthat/test-arg-ds.look.R +++ b/tests/testthat/test-arg-ds.look.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.look::arg::test errors") +# context("ds.look::arg::test errors") test_that("look_erros", { expect_error(expect_warning(ds.look(checks=TRUE), "'ds.look' is deprecated.", fixed = TRUE), " missing, please give an expression/function in inverted commas\n", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.ls.R b/tests/testthat/test-arg-ds.ls.R index f4405ee77..bf24b112d 100644 --- a/tests/testthat/test-arg-ds.ls.R +++ b/tests/testthat/test-arg-ds.ls.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("ds.ls::arg::setup") +# context("ds.ls::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ls::arg") +# context("ds.ls::arg") test_that("containing escape sequence", { res1 <- ds.ls(search.filter="_:A:_Environment") @@ -46,7 +47,7 @@ test_that("containing escape sequence", { # Shutdown # -context("ds.ls::arg::shutdown") +# context("ds.ls::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -58,4 +59,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.ls::arg::done") +# context("ds.ls::arg::done") diff --git a/tests/testthat/test-arg-ds.make.R b/tests/testthat/test-arg-ds.make.R index d4a4a6e0a..170b6f113 100644 --- a/tests/testthat/test-arg-ds.make.R +++ b/tests/testthat/test-arg-ds.make.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.make::arg::test errors") +# context("ds.make::arg::test errors") test_that("make_erros", { expect_error(ds.make(), "Please give the name of object to assign or an expression to evaluate and assign.!\n", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.matrix.R b/tests/testthat/test-arg-ds.matrix.R index 2201a4f40..c6cf9089e 100644 --- a/tests/testthat/test-arg-ds.matrix.R +++ b/tests/testthat/test-arg-ds.matrix.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrix::arg::test errors") +# context("ds.matrix::arg::test errors") test_that("matrix_erros", { res <- ds.matrix(mdata=NULL) diff --git a/tests/testthat/test-arg-ds.matrixDet.R b/tests/testthat/test-arg-ds.matrixDet.R index 37d633fa9..c598d81b7 100644 --- a/tests/testthat/test-arg-ds.matrixDet.R +++ b/tests/testthat/test-arg-ds.matrixDet.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDet::arg::test errors") +# context("ds.matrixDet::arg::test errors") test_that("matrixDet_erros", { res <- ds.matrixDet() diff --git a/tests/testthat/test-arg-ds.matrixDet.report.R b/tests/testthat/test-arg-ds.matrixDet.report.R index 6bb0bc6c3..d76b92392 100644 --- a/tests/testthat/test-arg-ds.matrixDet.report.R +++ b/tests/testthat/test-arg-ds.matrixDet.report.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDet.report::arg::test errors") +# context("ds.matrixDet.report::arg::test errors") test_that("ds.matixDet.report erros", { res <- ds.matrixDet.report(M1=NULL) diff --git a/tests/testthat/test-arg-ds.matrixDiag.R b/tests/testthat/test-arg-ds.matrixDiag.R index e022d23cf..0dc152ff2 100644 --- a/tests/testthat/test-arg-ds.matrixDiag.R +++ b/tests/testthat/test-arg-ds.matrixDiag.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDiag::arg::test errors") +# context("ds.matrixDiag::arg::test errors") test_that("matrixDiag_erros", { res <- ds.matrixDiag() diff --git a/tests/testthat/test-arg-ds.matrixDimnames.R b/tests/testthat/test-arg-ds.matrixDimnames.R index 02a1f33b5..c6da09344 100644 --- a/tests/testthat/test-arg-ds.matrixDimnames.R +++ b/tests/testthat/test-arg-ds.matrixDimnames.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixDimnames::arg::test errors") +# context("ds.matrixDimnames::arg::test errors") test_that("matrixDimnames_erros", { res <- ds.matrixDimnames() diff --git a/tests/testthat/test-arg-ds.matrixInvert.R b/tests/testthat/test-arg-ds.matrixInvert.R index 3718d6d07..dfed18dd6 100644 --- a/tests/testthat/test-arg-ds.matrixInvert.R +++ b/tests/testthat/test-arg-ds.matrixInvert.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixInvert::arg::test errors") +# context("ds.matrixInvert::arg::test errors") test_that("matrixInvert_erros", { res <- ds.matrixInvert() diff --git a/tests/testthat/test-arg-ds.matrixMult.R b/tests/testthat/test-arg-ds.matrixMult.R index 1ab873494..95564e0d5 100644 --- a/tests/testthat/test-arg-ds.matrixMult.R +++ b/tests/testthat/test-arg-ds.matrixMult.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixMult::arg::test errors") +# context("ds.matrixMult::arg::test errors") test_that("matrixMult_erros", { res <- ds.matrixMult() diff --git a/tests/testthat/test-arg-ds.matrixTranspose.R b/tests/testthat/test-arg-ds.matrixTranspose.R index ff94f60f0..d78c69041 100644 --- a/tests/testthat/test-arg-ds.matrixTranspose.R +++ b/tests/testthat/test-arg-ds.matrixTranspose.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.matrixTranspose::arg::test errors") +# context("ds.matrixTranspose::arg::test errors") test_that("matrixTranspose_erros", { res <- ds.matrixTranspose() diff --git a/tests/testthat/test-arg-ds.mean.R b/tests/testthat/test-arg-ds.mean.R index b28fdcbde..96ef958ba 100644 --- a/tests/testthat/test-arg-ds.mean.R +++ b/tests/testthat/test-arg-ds.mean.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.mean::arg::test errors") +# context("ds.mean::arg::test errors") test_that("mean_erros", { ds.asCharacter(x='D$LAB_TSC', newobj="not_a_numeric") diff --git a/tests/testthat/test-arg-ds.meanByClass.R b/tests/testthat/test-arg-ds.meanByClass.R index b829e05b9..c4de0a22b 100644 --- a/tests/testthat/test-arg-ds.meanByClass.R +++ b/tests/testthat/test-arg-ds.meanByClass.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","GENDER","DIS_DIAB","PM_B # Tests # -context("ds.meanByClass::arg::test errors") +# context("ds.meanByClass::arg::test errors") test_that("meanByClass_erros", { ds.asCharacter(x='D$GENDER', newobj="not_a_numeric") ds.asCharacter(x='D$GENDER', newobj="not_a_factor") diff --git a/tests/testthat/test-arg-ds.meanSdGp.R b/tests/testthat/test-arg-ds.meanSdGp.R index bacc72410..bac7b2c46 100644 --- a/tests/testthat/test-arg-ds.meanSdGp.R +++ b/tests/testthat/test-arg-ds.meanSdGp.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.meanSdGp::arg::test errors") +# context("ds.meanSdGp::arg::test errors") test_that("meanSdGp_erros", { expect_error(ds.meanSdGp(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.merge.R b/tests/testthat/test-arg-ds.merge.R index 5f6ccf385..4bb0bb8b4 100644 --- a/tests/testthat/test-arg-ds.merge.R +++ b/tests/testthat/test-arg-ds.merge.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.merge::arg::test errors") +# context("ds.merge::arg::test errors") test_that("merge_erros", { expect_error(ds.merge(), "Please provide the name (eg 'name1') of first dataframe to be merged (called x) ", fixed=TRUE) expect_error(ds.merge(x.name="A"), "Please provide the name (eg 'name2') of second dataframe to be merged (called y) ", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.message.R b/tests/testthat/test-arg-ds.message.R index 960e9811d..ea55ca136 100644 --- a/tests/testthat/test-arg-ds.message.R +++ b/tests/testthat/test-arg-ds.message.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.message::arg") +# context("ds.message::arg") test_that("request message for NULL", { expect_error(expect_warning(ds.message(NULL), "'ds.message' is deprecated.", fixed = TRUE), "Please provide the name of the studyside list object that holds the message\n in character format ie: 'object.name' in inverted commas", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.metadata.R b/tests/testthat/test-arg-ds.metadata.R index 6c05ee0a7..b31209f9a 100644 --- a/tests/testthat/test-arg-ds.metadata.R +++ b/tests/testthat/test-arg-ds.metadata.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.metadata::arg::setup") +# context("ds.metadata::arg::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.metadata::arg") +# context("ds.metadata::arg") test_that("missing variable", { expect_error(ds.metadata(x='E'), "The input object E is not defined in sim1, sim2, sim3!", fixed = TRUE) }) @@ -41,7 +42,7 @@ test_that("missing column", { # Tear down # -context("ds.metadata::arg::shutdown") +# context("ds.metadata::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -49,4 +50,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.metadata::arg::done") +# context("ds.metadata::arg::done") diff --git a/tests/testthat/test-arg-ds.mice.R b/tests/testthat/test-arg-ds.mice.R index 4c2c21d33..a90c9c166 100644 --- a/tests/testthat/test-arg-ds.mice.R +++ b/tests/testthat/test-arg-ds.mice.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.mice::arg::test errors") +# context("ds.mice::arg::test errors") test_that("mice_errors", { expect_error(ds.mice(), "Please provide the name of the dataframe or matrix that contains the incomplete data!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.names.R b/tests/testthat/test-arg-ds.names.R index 1c7fb10ae..f8c049106 100644 --- a/tests/testthat/test-arg-ds.names.R +++ b/tests/testthat/test-arg-ds.names.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.names::arg::test errors") +# context("ds.names::arg::test errors") test_that("simple ds.names errors", { expect_error(ds.names(), "Please provide the name of the input list!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.ns.R b/tests/testthat/test-arg-ds.ns.R index b63c944a2..56fb58f5a 100644 --- a/tests/testthat/test-arg-ds.ns.R +++ b/tests/testthat/test-arg-ds.ns.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("ds.ns::arg::setup") +# context("ds.ns::arg::setup") connect.studies.dataset.cnsim(list("PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ns::arg::test errors") +# context("ds.ns::arg::test errors") test_that("ns_errors", { expect_error(ds.ns(), "argument \"x\" is missing, with no default", fixed=TRUE) expect_error(ds.qlspline(x=NULL), "Please provide the name of the input variable x!", fixed=TRUE) @@ -34,7 +35,7 @@ test_that("ns_errors", { # Done # -context("ds.ns::arg::shutdown") +# context("ds.ns::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -42,4 +43,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.ns::arg::done") +# context("ds.ns::arg::done") diff --git a/tests/testthat/test-arg-ds.numNA.R b/tests/testthat/test-arg-ds.numNA.R index 62d1af6d9..be436303a 100644 --- a/tests/testthat/test-arg-ds.numNA.R +++ b/tests/testthat/test-arg-ds.numNA.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.numNA::arg::test errors") +# context("ds.numNA::arg::test errors") test_that("simple ds.numNA errors", { expect_error(ds.numNA(), "Please provide the name of a vector!") }) diff --git a/tests/testthat/test-arg-ds.qlspline.R b/tests/testthat/test-arg-ds.qlspline.R index 697b2898e..c7ff7650a 100644 --- a/tests/testthat/test-arg-ds.qlspline.R +++ b/tests/testthat/test-arg-ds.qlspline.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("ds.qlspline::arg::setup") +# context("ds.qlspline::arg::setup") connect.studies.dataset.cnsim(list("PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.qlspline::arg::test errors") +# context("ds.qlspline::arg::test errors") test_that("qlspline_errors", { expect_error(ds.qlspline(), "argument \"x\" is missing, with no default", fixed=TRUE) expect_error(ds.qlspline(x=NULL), "Please provide the name of the input variable x!", fixed=TRUE) @@ -36,7 +37,7 @@ test_that("qlspline_errors", { # Done # -context("ds.qlspline::arg::shutdown") +# context("ds.qlspline::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,4 +45,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.qlspline::arg::done") +# context("ds.qlspline::arg::done") diff --git a/tests/testthat/test-arg-ds.quantileMean.R b/tests/testthat/test-arg-ds.quantileMean.R index 2f94db2cc..4d1587628 100644 --- a/tests/testthat/test-arg-ds.quantileMean.R +++ b/tests/testthat/test-arg-ds.quantileMean.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list('LAB_HDL')) # Tests # -context("ds.quantileMean::arg::test errors") +# context("ds.quantileMean::arg::test errors") ds.asCharacter(x='D$LAB_HDL', newobj="not_a_numeric") test_that("quantileMean_erros", { expect_error(ds.quantileMean(), "Please provide the name of the input vector!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rBinom.R b/tests/testthat/test-arg-ds.rBinom.R index e031196a6..8d4100bde 100644 --- a/tests/testthat/test-arg-ds.rBinom.R +++ b/tests/testthat/test-arg-ds.rBinom.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rBinom::arg::test errors") +# context("ds.rBinom::arg::test errors") test_that("rBinom_erros", { error.message <- ds.rBinom(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.rNorm.R b/tests/testthat/test-arg-ds.rNorm.R index 0f3cb82c5..d4ec8075b 100644 --- a/tests/testthat/test-arg-ds.rNorm.R +++ b/tests/testthat/test-arg-ds.rNorm.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rNorm::arg::test errors") +# context("ds.rNorm::arg::test errors") test_that("rNorm_erros", { error.message <- ds.rNorm(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.rPois.R b/tests/testthat/test-arg-ds.rPois.R index 047064f97..707ca3813 100644 --- a/tests/testthat/test-arg-ds.rPois.R +++ b/tests/testthat/test-arg-ds.rPois.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rPois::arg::test errors") +# context("ds.rPois::arg::test errors") test_that("rPois_erros", { error.message <- ds.rPois(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.rUnif.R b/tests/testthat/test-arg-ds.rUnif.R index bfe839e64..be046e8e5 100644 --- a/tests/testthat/test-arg-ds.rUnif.R +++ b/tests/testthat/test-arg-ds.rUnif.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rUnif::arg::test errors") +# context("ds.rUnif::arg::test errors") test_that("rUnif_erros", { error.message <- ds.rUnif(seed.as.integer='Value') diff --git a/tests/testthat/test-arg-ds.ranksSecure.R b/tests/testthat/test-arg-ds.ranksSecure.R index 18778ccaf..fc6b99e1f 100644 --- a/tests/testthat/test-arg-ds.ranksSecure.R +++ b/tests/testthat/test-arg-ds.ranksSecure.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("ds.ranksSecure::arg::setup") +# context("ds.ranksSecure::arg::setup") connect.all.datasets() @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ranksSecure::arg::missing variable") +# context("ds.ranksSecure::arg::missing variable") test_that("missing variable", { expect_error(ds.ranksSecure("LAB_MISSING"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -36,7 +37,7 @@ test_that("missing variable", { expect_match(res.errors$study3, "* object 'LAB_MISSING' not found") }) -context("ds.ranksSecure::arg::NULL variable") +# context("ds.ranksSecure::arg::NULL variable") test_that("NULL variable", { DSI::datashield.assign.expr(conns = ds.test_env$connections, symbol = "LAB_NULL", expr = "NULL") @@ -57,7 +58,7 @@ test_that("NULL variable", { expect_match(res.errors$study3, "* Error in stats::complete.cases\\(input.var\\) : \n no input has determined the number of cases") }) -context("ds.ranksSecure::arg::'text' variable") +# context("ds.ranksSecure::arg::'text' variable") test_that("'text' variable", { expect_error(ds.ranksSecure("D$CHARACTER"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -69,12 +70,12 @@ test_that("'text' variable", { expect_match(res.errors$study3, "* Error in \\(1 - h\\) \\* qs\\[i\\] : non-numeric argument to binary operator") }) -context("ds.ranksSecure::arg::'logical' variable") +# context("ds.ranksSecure::arg::'logical' variable") test_that("'logical' variable", { expect_error(ds.ranksSecure("D$LOGICAL"), "FAILED: one of the extreme quantile estimates is NA probably because of a cluster of values at one end of the range of possible values. Try setting a narrower range of quantile values via the argument", fixed = TRUE) }) -context("ds.ranksSecure::arg::'integer factor' variable") +# context("ds.ranksSecure::arg::'integer factor' variable") test_that("'integer factor' variable", { expect_error(expect_warning(ds.ranksSecure("D$INTEGER_FACTOR"), "no non-missing arguments to max; returning -Inf", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -90,7 +91,7 @@ test_that("'integer factor' variable", { # Done # -context("ds.ranksSecure::arg::shutdown") +# context("ds.ranksSecure::arg::shutdown") test_that("setup", { ds_expect_variables(c("D", "LAB_NULL", "input.mean.sd.df", "min.max.df", "summary.ranks.df", "testvar.ranks")) @@ -98,4 +99,4 @@ test_that("setup", { disconnect.all.datasets() -context("ds.ranksSecure::arg::done") +# context("ds.ranksSecure::arg::done") diff --git a/tests/testthat/test-arg-ds.rbind.R b/tests/testthat/test-arg-ds.rbind.R index e25b36a19..3a4ed9f27 100644 --- a/tests/testthat/test-arg-ds.rbind.R +++ b/tests/testthat/test-arg-ds.rbind.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.rbind::arg::test errors") +# context("ds.rbind::arg::test errors") test_that("rbind_erros", { expect_error(ds.rbind(), "Please provide a vector of character strings holding the name of the input elements!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.reShape.R b/tests/testthat/test-arg-ds.reShape.R index f38f9ab7c..ed8e8102b 100644 --- a/tests/testthat/test-arg-ds.reShape.R +++ b/tests/testthat/test-arg-ds.reShape.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.reShape::arg::test errors") +# context("ds.reShape::arg::test errors") test_that("reShape_erros", { expect_error(ds.reShape(), "Please provide the name of the list that holds the input vectors!", fixed=TRUE) expect_error(ds.reShape(data.name="test", sep=TRUE), "'sep' must be a character string", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.recodeLevels.R b/tests/testthat/test-arg-ds.recodeLevels.R index 597b6e9ce..88b4b36e5 100644 --- a/tests/testthat/test-arg-ds.recodeLevels.R +++ b/tests/testthat/test-arg-ds.recodeLevels.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("PM_BMI_CATEGORICAL", "LAB_TSC")) # Tests # -context("ds.recodeLevels::arg::test errors") +# context("ds.recodeLevels::arg::test errors") test_that("recodeLevels_erros", { expect_error(expect_warning(ds.recodeLevels(), "'ds.recodeLevels' is deprecated.", fixed = TRUE), " End of process!", fixed=TRUE) expect_error(expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL'), "'ds.recodeLevels' is deprecated.", fixed = TRUE), " End of process!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.recodeValues.R b/tests/testthat/test-arg-ds.recodeValues.R index a5b747dc4..74a2da507 100644 --- a/tests/testthat/test-arg-ds.recodeValues.R +++ b/tests/testthat/test-arg-ds.recodeValues.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.recodeValues::arg::test errors") +# context("ds.recodeValues::arg::test errors") test_that("recodeValues_erros", { expect_error(ds.recodeValues(), "Please provide the name of the variable to be recoded: eg 'xxx'", fixed=TRUE) expect_error(ds.recodeValues('D$LAB_TSC'), "Please provide a vector in the 'values2replace.vector' argument specifying\n the values to be replaced eg c(1,7)", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rep.R b/tests/testthat/test-arg-ds.rep.R index 0ac3a0dfb..f9c2ec6ba 100644 --- a/tests/testthat/test-arg-ds.rep.R +++ b/tests/testthat/test-arg-ds.rep.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::arg::setup") +# context("ds.rep::arg::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -20,7 +21,7 @@ connect.studies.dataset.survival(list("survtime", "time.id", "female")) # Tests # -context("ds.rep::arg::test errors") +# context("ds.rep::arg::test errors") test_that("ds.rep erros", { res <- ds.rep() @@ -32,8 +33,8 @@ test_that("ds.rep erros", { # Done # -context("ds.rep::arg::shutdown") +# context("ds.rep::arg::shutdown") disconnect.studies.dataset.survival() -context("ds.rep::arg::done") +# context("ds.rep::arg::done") diff --git a/tests/testthat/test-arg-ds.replaceNA.R b/tests/testthat/test-arg-ds.replaceNA.R index b768a93fa..acd8c7b7e 100644 --- a/tests/testthat/test-arg-ds.replaceNA.R +++ b/tests/testthat/test-arg-ds.replaceNA.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.replaceNA::arg::test errors") +# context("ds.replaceNA::arg::test errors") test_that("simple ds.replaceNA errors", { expect_error(ds.replaceNA(), "Please provide the name of a vector!", fixed=TRUE) expect_error(ds.replaceNA(x="D$LAB_TSC"), "Please provide a list of replacement values!", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rm.R b/tests/testthat/test-arg-ds.rm.R index ee4f5e3fb..bb674bca1 100644 --- a/tests/testthat/test-arg-ds.rm.R +++ b/tests/testthat/test-arg-ds.rm.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. @@ -18,7 +19,7 @@ connect.studies.dataset.survival(list("survtime", "time.id", "female")) # Tests # -context("ds.rm::arg::test errors") +# context("ds.rm::arg::test errors") test_that("ds.rm erros", { expect_error(ds.rm(), "Please provide the names of the objects to be deleted (eg 'object.name') as the x.names argument", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.rowColCalc.R b/tests/testthat/test-arg-ds.rowColCalc.R index 9fc14230f..76b8604bb 100644 --- a/tests/testthat/test-arg-ds.rowColCalc.R +++ b/tests/testthat/test-arg-ds.rowColCalc.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) # Tests # -context("ds.rowColCalc::arg::test errors") +# context("ds.rowColCalc::arg::test errors") test_that("rowColCalc_errors", { expect_error(ds.rowColCalc(), "Please provide the name of a data.frame or matrix!", fixed=TRUE) expect_error(ds.rowColCalc(x='D', newobj="rsum_hdl_tsc"), "'operation' = NULL. Please set it to 'rowSums', 'colSums', 'rowMeans' or 'colMeans'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.sample.R b/tests/testthat/test-arg-ds.sample.R index 0d14e79f4..f84f4c3e7 100644 --- a/tests/testthat/test-arg-ds.sample.R +++ b/tests/testthat/test-arg-ds.sample.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.sample::arg::setup") +# context("ds.sample::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -20,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.sample::arg::test errors") +# context("ds.sample::arg::test errors") test_that("cov_erros", { res1 <- ds.sample() expect_equal(res1, 'Error: x must denote a character string naming the serverside object to be sampled or an integer N denoting permute 1:N', fixed=TRUE) @@ -34,7 +35,7 @@ test_that("cov_erros", { # Shutdown # -context("ds.sample::arg::shutdown") +# context("ds.sample::arg::shutdown") disconnect.studies.dataset.cnsim() @@ -42,4 +43,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.sample::arg::done") +# context("ds.sample::arg::done") diff --git a/tests/testthat/test-arg-ds.seq.R b/tests/testthat/test-arg-ds.seq.R index 7ba77b7b0..3d047e7e4 100644 --- a/tests/testthat/test-arg-ds.seq.R +++ b/tests/testthat/test-arg-ds.seq.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.seq::arg::test errors") +# context("ds.seq::arg::test errors") test_that("seq_erros", { expect_error(ds.seq(FROM.value.char="Test"), "object 'Test' not found", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.setSeed.R b/tests/testthat/test-arg-ds.setSeed.R index 441275817..1bf41b5ca 100644 --- a/tests/testthat/test-arg-ds.setSeed.R +++ b/tests/testthat/test-arg-ds.setSeed.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.setSeed::arg::test errors") +# context("ds.setSeed::arg::test errors") test_that("setSeed_erros", { res <- ds.setSeed(seed.as.integer="Test") diff --git a/tests/testthat/test-arg-ds.skewness.R b/tests/testthat/test-arg-ds.skewness.R index cc1751a69..6a9440cc7 100644 --- a/tests/testthat/test-arg-ds.skewness.R +++ b/tests/testthat/test-arg-ds.skewness.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.skewness::arg::setup") +# context("ds.skewness::arg::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.skewness::arg::test errors") +# context("ds.skewness::arg::test errors") test_that("skewness_erros", { expect_error(ds.skewness(), "Please provide the name of the input vector!", fixed=TRUE) expect_error(ds.skewness(x='D$LAB_TSC', type='datashield'), "Function argument \"type\" has to be either \"both\", \"combine\" or \"split\"", fixed=TRUE) @@ -36,7 +37,7 @@ test_that("skewness_erros", { # Done # -context("ds.skewness::arg::shutdown") +# context("ds.skewness::arg::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,4 +45,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.skewness::arg::done") +# context("ds.skewness::arg::done") diff --git a/tests/testthat/test-arg-ds.subset.R b/tests/testthat/test-arg-ds.subset.R index a314d4906..65a96c814 100644 --- a/tests/testthat/test-arg-ds.subset.R +++ b/tests/testthat/test-arg-ds.subset.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("DIS_DIAB","PM_BMI_CONTINUOUS","LAB_HDL", "GE # Tests # -context("ds.subset::arg::test errors") +# context("ds.subset::arg::test errors") test_that("subset_erros", { expect_error(expect_warning(ds.subset(), "'ds.subset' is deprecated.", fixed = TRUE), "Please provide the name of the object to subset from!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.subsetByClass.R b/tests/testthat/test-arg-ds.subsetByClass.R index 5aca7abfd..9645b195e 100644 --- a/tests/testthat/test-arg-ds.subsetByClass.R +++ b/tests/testthat/test-arg-ds.subsetByClass.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.subsetByClass::arg::test errors") +# context("ds.subsetByClass::arg::test errors") test_that("subsetByClass_erros", { expect_error(expect_warning(ds.subsetByClass(), "'ds.subsetByClass' is deprecated.", fixed = TRUE), "Please provide the name of the input data frame or factor!", fixed=TRUE) expect_error(expect_warning(ds.subsetByClass(x='D$LAB_TSC'), "'ds.subsetByClass' is deprecated.", fixed = TRUE), "The object to subset from must be a 'data.frame' or a 'factor'.", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.summary.R b/tests/testthat/test-arg-ds.summary.R index 5a2aa982c..e3d386568 100644 --- a/tests/testthat/test-arg-ds.summary.R +++ b/tests/testthat/test-arg-ds.summary.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.summary::arg::test errors") +# context("ds.summary::arg::test errors") test_that("summary_erros", { expect_error(ds.summary(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.table.R b/tests/testthat/test-arg-ds.table.R index b18ff9497..094cf97ce 100644 --- a/tests/testthat/test-arg-ds.table.R +++ b/tests/testthat/test-arg-ds.table.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. @@ -18,14 +19,14 @@ connect.studies.dataset.cnsim(list("DIS_CVA", "DIS_AMI", "LAB_TSC", "LAB_HDL")) # Tests # -context("ds.table::arg::test rvar has value") +# context("ds.table::arg::test rvar has value") test_that("table rvar has value", { res <- ds.table() expect_equal(res, "Error: rvar must have a value which is a character string naming the row variable for the table", fixed=TRUE) }) -context("ds.table::arg::test rvar is not a variable") +# context("ds.table::arg::test rvar is not a variable") test_that("table rvar is not a variable", { expect_error(ds.table(rvar="D$NOT_VARIABLE"), "The input object D$NOT_VARIABLE is not defined in sim1, sim2, sim3!", fixed = TRUE) @@ -34,14 +35,14 @@ test_that("table rvar is not a variable", { expect_length(res.errors, 0) }) -context("ds.table::arg::test cvar has value") +# context("ds.table::arg::test cvar has value") test_that("table cvar has value", { res <- ds.table(rvar="D$LAB_TSC", cvar=30) expect_equal(res, "Error: if cvar is not null, it must have a value which is a character string naming the column variable for the table", fixed=TRUE) }) -context("ds.table::arg::test cvar is not a variable") +# context("ds.table::arg::test cvar is not a variable") test_that("table cvar is not a variable", { expect_error(ds.table(rvar="D$DIS_CVA", cvar="D$NOT_VARIABLE"), "The input object D$NOT_VARIABLE is not defined in sim1, sim2, sim3!", fixed = TRUE) @@ -50,14 +51,14 @@ test_that("table cvar is not a variable", { expect_length(res.errors, 0) }) -context("ds.table::arg::test stvar has value") +# context("ds.table::arg::test stvar has value") test_that("table stvar has value", { res <- ds.table(rvar="D$LAB_TSC", cvar=NULL, stvar=25) expect_equal(res, "Error: if stvar is not null, it must have a value which is a character string naming the variable coding separate tables for the table", fixed=TRUE) }) -context("ds.table::arg::test stvar is not a variable") +# context("ds.table::arg::test stvar is not a variable") test_that("table stvar is not a variable", { expect_error(ds.table(rvar="D$DIS_CVA", cvar="D$DIS_AMI", stvar="D$NOT_VARIABLE"), "The input object D$NOT_VARIABLE is not defined in sim1, sim2, sim3!", fixed = TRUE) @@ -66,12 +67,12 @@ test_that("table stvar is not a variable", { expect_length(res.errors, 0) }) -context("ds.table::arg::test stvar has CORRECT value") +# context("ds.table::arg::test stvar has CORRECT value") test_that("table useNA has value", { expect_error(ds.table(rvar="D$LAB_TSC", cvar=NULL, stvar=NULL, useNA = c("BEN")), "useNA must be either 'no' or 'always'.", fixed = TRUE) }) -context("ds.table::arg::test force.nfilter has value") +# context("ds.table::arg::test force.nfilter has value") test_that("table force.nfilter has value", { expect_error(ds.table(rvar="D$LAB_TSC", cvar=NULL, stvar=NULL, useNA = c("ifany"), force.nfilter =30), "useNA must be either 'no' or 'always'.", fixed = TRUE) }) diff --git a/tests/testthat/test-arg-ds.table1D.R b/tests/testthat/test-arg-ds.table1D.R index b0bf5e6d1..56c17dd4e 100644 --- a/tests/testthat/test-arg-ds.table1D.R +++ b/tests/testthat/test-arg-ds.table1D.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("DIS_CVA","GENDER")) # Tests # -context("ds.table1D::arg::test errors") +# context("ds.table1D::arg::test errors") test_that("table1D_erros", { expect_error(expect_warning(ds.table1D(), "'ds.table1D' is deprecated.", fixed = TRUE), "Please provide the name of the input vector!", fixed=TRUE) expect_error(expect_warning(ds.table1D(x='D$GENDER', type="datashield"), "'ds.table1D' is deprecated.", fixed = TRUE), "Function argument 'type' has to be either 'combine' or 'split'", fixed=TRUE) diff --git a/tests/testthat/test-arg-ds.table2D.R b/tests/testthat/test-arg-ds.table2D.R index 35fa39dba..e7b0623ee 100644 --- a/tests/testthat/test-arg-ds.table2D.R +++ b/tests/testthat/test-arg-ds.table2D.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.table2D::arg::test errors") +# context("ds.table2D::arg::test errors") test_that("table2D_erros", { expect_error(expect_warning(ds.table2D(), "'ds.table2D' is deprecated.", fixed = TRUE), "Please provide the name of the x vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.tapply.R b/tests/testthat/test-arg-ds.tapply.R index 243de56e0..5ac42edf5 100644 --- a/tests/testthat/test-arg-ds.tapply.R +++ b/tests/testthat/test-arg-ds.tapply.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) # Tests # -context("ds.tapply::arg::test errors") +# context("ds.tapply::arg::test errors") test_that("tapply_erros", { res1 <- ds.tapply() diff --git a/tests/testthat/test-arg-ds.tapply.assign.R b/tests/testthat/test-arg-ds.tapply.assign.R index 787628d19..14ea83890 100644 --- a/tests/testthat/test-arg-ds.tapply.assign.R +++ b/tests/testthat/test-arg-ds.tapply.assign.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) # Tests # -context("ds.tapply.assign::arg::test errors") +# context("ds.tapply.assign::arg::test errors") test_that("tapply_erros", { res1 <- ds.tapply.assign() diff --git a/tests/testthat/test-arg-ds.testObjExists.R b/tests/testthat/test-arg-ds.testObjExists.R index c2f657810..bf01cc77a 100644 --- a/tests/testthat/test-arg-ds.testObjExists.R +++ b/tests/testthat/test-arg-ds.testObjExists.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.testObjExists::arg::test errors") +# context("ds.testObjExists::arg::test errors") test_that("testObjExists_erros", { res <- ds.testObjExists() diff --git a/tests/testthat/test-arg-ds.unList.R b/tests/testthat/test-arg-ds.unList.R index bddb5e06d..2d3aa4877 100644 --- a/tests/testthat/test-arg-ds.unList.R +++ b/tests/testthat/test-arg-ds.unList.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.unList::arg::test errors") +# context("ds.unList::arg::test errors") test_that("unList_erros", { expect_error(ds.unList(), "Please provide the name of the input vector!", fixed=TRUE) }) diff --git a/tests/testthat/test-arg-ds.unique.R b/tests/testthat/test-arg-ds.unique.R index bd619015e..a0e112a59 100644 --- a/tests/testthat/test-arg-ds.unique.R +++ b/tests/testthat/test-arg-ds.unique.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. @@ -18,12 +19,12 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.unique::arg::no arguments") +# context("ds.unique::arg::no arguments") test_that("simple ds.unique no arguments", { expect_error(ds.unique(), "x.name=NULL. Please provide the names of the objects to de-duplicated!", fixed = TRUE) }) -context("ds.unique::arg::NULL arguments") +# context("ds.unique::arg::NULL arguments") test_that("simple ds.unique NULL arguments", { expect_error(ds.unique(NULL), "x.name=NULL. Please provide the names of the objects to de-duplicated!", fixed = TRUE) }) diff --git a/tests/testthat/test-arg-ds.var.R b/tests/testthat/test-arg-ds.var.R index 71c2d89e8..8ececd0d0 100644 --- a/tests/testthat/test-arg-ds.var.R +++ b/tests/testthat/test-arg-ds.var.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC")) # Tests # -context("ds.var::arg::test errors") +# context("ds.var::arg::test errors") test_that("var_erros", { ds.asCharacter(x='D$LAB_TSC', newobj="not_a_numeric") diff --git a/tests/testthat/test-arg-ds.vectorCalc.R b/tests/testthat/test-arg-ds.vectorCalc.R index 7a572365b..4c331b869 100644 --- a/tests/testthat/test-arg-ds.vectorCalc.R +++ b/tests/testthat/test-arg-ds.vectorCalc.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. @@ -18,7 +19,7 @@ connect.studies.dataset.survival(list("survtime")) # Tests # -context("ds.vectorCalc::arg::test errors") +# context("ds.vectorCalc::arg::test errors") test_that("ds.vectorCalc erros", { expect_error(expect_warning(ds.vectorCalc(), "'ds.vectorCalc' is deprecated.\nUse 'ds.make' instead.", fixed = TRUE), "x=NULL. Please provide the names of the objects to combine!", fixed=TRUE) diff --git a/tests/testthat/test-datachk-ANTHRO.R b/tests/testthat/test-datachk-ANTHRO.R index 2789755fa..41a53637d 100644 --- a/tests/testthat/test-datachk-ANTHRO.R +++ b/tests/testthat/test-datachk-ANTHRO.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("ANTHRO::datachk::setup") +# context("ANTHRO::datachk::setup") connect.studies.dataset.anthro(list('age', 'sex', 'weight', 'height', 'muac')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ANTHRO::datachk") +# context("ANTHRO::datachk") test_that("Check ANTHRO dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -159,7 +160,7 @@ test_that("Check ANTHRO dataset", { # Tear down # -context("ANTHRO::datachk::shutdown") +# context("ANTHRO::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -171,4 +172,4 @@ disconnect.studies.dataset.anthro() # Done # -context("ANTHRO::datachk::done") +# context("ANTHRO::datachk::done") diff --git a/tests/testthat/test-datachk-CLUSTER_INT.R b/tests/testthat/test-datachk-CLUSTER_INT.R index 8fc7deff2..d86eddd1a 100644 --- a/tests/testthat/test-datachk-CLUSTER_INT.R +++ b/tests/testthat/test-datachk-CLUSTER_INT.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("CLUSTER_INT::datachk::setup") +# context("CLUSTER_INT::datachk::setup") connect.studies.dataset.cluster.int(list("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "nPatients", "Male", "age", "BMI", "diabetes", "incid_rate", "private")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("CLUSTER_INT::datachk") +# context("CLUSTER_INT::datachk") test_that("Check CLUSTER INT dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -319,7 +320,7 @@ test_that("Check CLUSTER INT dataset", { # Tear down # -context("CLUSTER_INT::datachk::shutdown") +# context("CLUSTER_INT::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -327,4 +328,4 @@ test_that("shutdown", { disconnect.studies.dataset.cluster.int() -context("CLUSTER_INT::datachk::done") +# context("CLUSTER_INT::datachk::done") diff --git a/tests/testthat/test-datachk-CLUSTER_SLO.R b/tests/testthat/test-datachk-CLUSTER_SLO.R index 3c61c9cb7..842a5d409 100644 --- a/tests/testthat/test-datachk-CLUSTER_SLO.R +++ b/tests/testthat/test-datachk-CLUSTER_SLO.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("CLUSTER_SLO::datachk::setup") +# context("CLUSTER_SLO::datachk::setup") connect.studies.dataset.cluster.slo(list("idSurgery", "trtGrp", "intSurgery", "nDoctors", "idDoctor", "intDoctor", "sloDoctor", "nPatients", "Male", "age", "BMI", "private", "diabetes", "incid_rate")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("CLUSTER_SLO::datachk") +# context("CLUSTER_SLO::datachk") test_that("Check CLUSTER SLO dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -319,7 +320,7 @@ test_that("Check CLUSTER SLO dataset", { # Tear down # -context("CLUSTER_SLO::datachk::shutdown") +# context("CLUSTER_SLO::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -327,4 +328,4 @@ test_that("shutdown", { disconnect.studies.dataset.cluster.slo() -context("CLUSTER_SLO::datachk::done") +# context("CLUSTER_SLO::datachk::done") diff --git a/tests/testthat/test-datachk-CNSIM.R b/tests/testthat/test-datachk-CNSIM.R index 7296f51b7..afdfc8214 100644 --- a/tests/testthat/test-datachk-CNSIM.R +++ b/tests/testthat/test-datachk-CNSIM.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("CNSIM::datachk::setup") +# context("CNSIM::datachk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("CNSIM::datachk") +# context("CNSIM::datachk") test_that("Check CNSIM dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -378,7 +379,7 @@ test_that("Check CNSIM dataset", { # Tear down # -context("CNSIM::datachk::shutdown") +# context("CNSIM::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -386,4 +387,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("CNSIM::datachk::done") +# context("CNSIM::datachk::done") diff --git a/tests/testthat/test-datachk-DISCORDANT.R b/tests/testthat/test-datachk-DISCORDANT.R index bb6c06a21..5254897b2 100644 --- a/tests/testthat/test-datachk-DISCORDANT.R +++ b/tests/testthat/test-datachk-DISCORDANT.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("DISCORDANT::datachk::setup") +# context("DISCORDANT::datachk::setup") connect.discordant.dataset.simple(list('A', 'B', 'C')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("DISCORDANT::datachk") +# context("DISCORDANT::datachk") test_that("Check DISCORDANT dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -123,7 +124,7 @@ test_that("Check DISCORDANT dataset", { # Tear down # -context("DISCORDANT::datachk::shutdown") +# context("DISCORDANT::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -135,4 +136,4 @@ disconnect.discordant.dataset.simple() # Done # -context("DISCORDANT::datachk::done") +# context("DISCORDANT::datachk::done") diff --git a/tests/testthat/test-datachk-DNSIM.R b/tests/testthat/test-datachk-DNSIM.R index 73421dba4..f3a9e75c7 100644 --- a/tests/testthat/test-datachk-DNSIM.R +++ b/tests/testthat/test-datachk-DNSIM.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("DASIM::datachk::setup") +# context("DASIM::datachk::setup") connect.studies.dataset.dasim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_FASTING', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("DASIM::datachk") +# context("DASIM::datachk") test_that("Check DASIM dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -259,7 +260,7 @@ test_that("Check DASIM dataset", { # Tear down # -context("DASIM::datachk::shutdown") +# context("DASIM::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -267,4 +268,4 @@ test_that("shutdown", { disconnect.studies.dataset.dasim() -context("DASIM::datachk::done") +# context("DASIM::datachk::done") diff --git a/tests/testthat/test-datachk-FACTOR_LEVELS.R b/tests/testthat/test-datachk-FACTOR_LEVELS.R index d1db51fec..927e1cab6 100644 --- a/tests/testthat/test-datachk-FACTOR_LEVELS.R +++ b/tests/testthat/test-datachk-FACTOR_LEVELS.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("FACTOR_LEVELS::datachk::setup") +# context("FACTOR_LEVELS::datachk::setup") connect.testing.dataset.factor_levels() @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("FACTOR_LEVELS::datachk") +# context("FACTOR_LEVELS::datachk") test_that("Check FACTOR_LEVELS dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -259,7 +260,7 @@ test_that("Check FACTOR_LEVELS dataset", { # Tear down # -context("FACTOR_LEVELS::datachk::shutdown") +# context("FACTOR_LEVELS::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -267,4 +268,4 @@ test_that("shutdown", { disconnect.testing.dataset.factor_levels() -context("FACTOR_LEVELS::datachk::done") +# context("FACTOR_LEVELS::datachk::done") diff --git a/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.R b/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.R index bc8c12bce..0d28eff58 100644 --- a/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.R +++ b/tests/testthat/test-datachk-SURVIVAL_EXPAND_WITH_MISSING.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("SURVIVAL_EXPAND_WITH_MISSING::datachk::setup") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk::setup") connect.studies.dataset.survival(list('id', 'study.id', 'time.id', 'starttime', 'endtime', 'survtime', 'cens', 'age.60', 'female', 'noise.56', 'pm10.16', 'bmi.26')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("SURVIVAL_EXPAND_WITH_MISSING::datachk") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk") test_that("Check SURVIVAL_EXPAND_WITH_MISSING dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -279,7 +280,7 @@ test_that("Check SURVIVAL_EXPAND_WITH_MISSING dataset", { # Tear down # -context("SURVIVAL_EXPAND_WITH_MISSING::datachk::shutdown") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -291,4 +292,4 @@ disconnect.studies.dataset.survival() # Done # -context("SURVIVAL_EXPAND_WITH_MISSING::datachk::done") +# context("SURVIVAL_EXPAND_WITH_MISSING::datachk::done") diff --git a/tests/testthat/test-datachk-TESTING.R b/tests/testthat/test-datachk-TESTING.R index 5cc2332d0..f89d43643 100644 --- a/tests/testthat/test-datachk-TESTING.R +++ b/tests/testthat/test-datachk-TESTING.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("TESTING::datachk::setup") +# context("TESTING::datachk::setup") connect.all.datasets() @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("TESTING::datachk") +# context("TESTING::datachk") test_that("Check TESTING dataset", { res.class <- ds.class(x='D') expect_length(res.class, 3) @@ -419,7 +420,7 @@ test_that("Check TESTING dataset", { # Tear down # -context("TESTING::datachk::shutdown") +# context("TESTING::datachk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -427,4 +428,4 @@ test_that("shutdown", { disconnect.all.datasets() -context("TESTING::datachk::done") +# context("TESTING::datachk::done") diff --git a/tests/testthat/test-disc-ds.cor.R b/tests/testthat/test-disc-ds.cor.R index eb61ada6f..88da21bbd 100644 --- a/tests/testthat/test-disc-ds.cor.R +++ b/tests/testthat/test-disc-ds.cor.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.cor::disc::setup") +# context("ds.cor::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.cor::disc") +# context("ds.cor::disc") test_that("simple D3 setup", { ds.dataFrameSubset('D',V1.name = 'D$GENDER', V2.name = '0', Boolean.operator = '==', newobj='D1') ds.dataFrameSubset('D1',V1.name = 'D1$LAB_TSC', V2.name = '3.5', Boolean.operator = '<', newobj='D2') @@ -107,7 +108,7 @@ test_that("simple disc test, naAction='pairwise.complete', type='combine'", { # Done # -context("ds.cor::disc::shutdown") +# context("ds.cor::disc::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D1", "D2", "D3")) @@ -115,4 +116,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.cor::disc::done") +# context("ds.cor::disc::done") diff --git a/tests/testthat/test-disc-ds.cov.R b/tests/testthat/test-disc-ds.cov.R index 751d54bf9..2807a7b1c 100644 --- a/tests/testthat/test-disc-ds.cov.R +++ b/tests/testthat/test-disc-ds.cov.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.cov::disc::setup") +# context("ds.cov::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.cov::disc") +# context("ds.cov::disc") test_that("simple D3 setup", { ds.dataFrameSubset('D',V1.name = 'D$GENDER', V2.name = '0', Boolean.operator = '==', newobj='D1') ds.dataFrameSubset('D1',V1.name = 'D1$LAB_TSC', V2.name = '3.5', Boolean.operator = '<', newobj='D2') @@ -106,7 +107,7 @@ test_that("simple disc test, naAction='pairwise.complete', type='combine'", { # Done # -context("ds.cov::disc::shutdown") +# context("ds.cov::disc::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D1", "D2", "D3")) @@ -114,4 +115,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.cov::disc::done") +# context("ds.cov::disc::done") diff --git a/tests/testthat/test-disc-ds.levels.R b/tests/testthat/test-disc-ds.levels.R index 6f00f1198..95d0c60b5 100644 --- a/tests/testthat/test-disc-ds.levels.R +++ b/tests/testthat/test-disc-ds.levels.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.levels::disc::setup") +# context("ds.levels::disc::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.levels::disc") +# context("ds.levels::disc") test_that("simple levels", { # res <- ds.levels("D$GENDER") @@ -51,7 +52,7 @@ test_that("simple levels", { # Done # -context("ds.levels::disc::shutdown") +# context("ds.levels::disc::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -59,4 +60,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.levels::disc::done") +# context("ds.levels::disc::done") diff --git a/tests/testthat/test-disc-ds.mean.R b/tests/testthat/test-disc-ds.mean.R index f1b690c9d..cb8311d79 100644 --- a/tests/testthat/test-disc-ds.mean.R +++ b/tests/testthat/test-disc-ds.mean.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.mean::disc::type=both") +# context("ds.mean::disc::type=both") test_that("mean values [both]", { # myvectors <- c("D$LAB_TSC", "D$LAB_TRIG") # ds.dataFrame(x=myvectors, newobj="unsubset_df") diff --git a/tests/testthat/test-disc-ds.meanByClass.R b/tests/testthat/test-disc-ds.meanByClass.R index 2b6147f8c..b1e7cedb6 100644 --- a/tests/testthat/test-disc-ds.meanByClass.R +++ b/tests/testthat/test-disc-ds.meanByClass.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("ds.meanByClass::disc::setup") +# context("ds.meanByClass::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","GENDER","DIS_DIAB","PM_BMI_CATEGORICAL")) @@ -20,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","GENDER","DIS_DIAB","PM_B # Tests # -context("ds.meanByClass::disc::test errors") +# context("ds.meanByClass::disc::test errors") test_that("meanByClass_erros", { # expect_error(ds.meanByClass(x='D', outvar='LAB_HDL', covar='GENDER', type='split'), 'Failed to get levels from study: FAILED: Result less than nfilter.subset', fixed=TRUE) }) @@ -29,7 +30,7 @@ test_that("meanByClass_erros", { # Tear down # -context("ds.meanByClass::disc::teardown") +# context("ds.meanByClass::disc::teardown") disconnect.studies.dataset.cnsim() @@ -37,4 +38,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.meanByClass::disc::done") +# context("ds.meanByClass::disc::done") diff --git a/tests/testthat/test-disc-ds.sample.R b/tests/testthat/test-disc-ds.sample.R index 08cc01c7f..ce74288a7 100644 --- a/tests/testthat/test-disc-ds.sample.R +++ b/tests/testthat/test-disc-ds.sample.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.sample::disc::setup") +# context("ds.sample::disc::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -20,7 +21,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.sample::disc::test disclosure") +# context("ds.sample::disc::test disclosure") test_that("cov_erros", { expect_error(ds.sample(x="This_line_is_very_very_very_very_very_very_long", size=1234, newobj="obj1"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) res1.errors <- DSI::datashield.errors() @@ -64,7 +65,7 @@ test_that("cov_erros", { # Shutdown # -context("ds.sample::disc::shutdown") +# context("ds.sample::disc::shutdown") disconnect.studies.dataset.cnsim() @@ -72,4 +73,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.sample::disc::done") +# context("ds.sample::disc::done") diff --git a/tests/testthat/test-disc-ds.table.R b/tests/testthat/test-disc-ds.table.R index f82116940..b51a75f91 100644 --- a/tests/testthat/test-disc-ds.table.R +++ b/tests/testthat/test-disc-ds.table.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. @@ -13,7 +14,7 @@ # Set up - Phase 1 # -context("ds.table::disc::setup::phase 1") +# context("ds.table::disc::setup::phase 1") connect.all.datasets() @@ -25,7 +26,7 @@ test_that("setup", { # Tests - Phase 1 # -context("ds.table::disc::tests::phase 1::table.assign=FALSE") +# context("ds.table::disc::tests::phase 1::table.assign=FALSE") test_that("table disclosure table.assign=FALSE", { ds.asFactor(input.var.name="D$FACTOR_CHARACTER", newobj.name="factorCharacter") ds.asFactor(input.var.name="D$FACTOR_INTEGER", newobj.name="factorInteger") @@ -43,7 +44,7 @@ test_that("table disclosure table.assign=FALSE", { expect_equal(table.res$validity.message[4], "Study3: No errors reported from this study", fixed = TRUE) }) -context("ds.table::disc::tests::phase 1::table.assign=TRUE") +# context("ds.table::disc::tests::phase 1::table.assign=TRUE") test_that("table disclosure table.assign=TRUE", { ds.asFactor(input.var.name="D$FACTOR_CHARACTER", newobj.name="factorCharacter") ds.asFactor(input.var.name="D$FACTOR_INTEGER", newobj.name="factorInteger") @@ -55,7 +56,7 @@ test_that("table disclosure table.assign=TRUE", { expect_length(table.res, 0) }) -context("ds.table::disc::test rvar is big numeric") +# context("ds.table::disc::test rvar is big numeric") test_that("table rvar is big numeric", { expect_error(ds.table(rvar="D$NUMERIC"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -71,7 +72,7 @@ test_that("table rvar is big numeric", { # Shutdown - Phase 1 # -context("ds.table::disc::shutdown::phase 1") +# context("ds.table::disc::shutdown::phase 1") test_that("setup", { ds_expect_variables(c("D", "factorCharacter", "factorInteger", "tablesource", "new_table2")) @@ -83,7 +84,7 @@ disconnect.all.datasets() # Set up - Phase 2 # -context("ds.table::disc::setup::phase 2") +# context("ds.table::disc::setup::phase 2") connect.studies.dataset.cnsim(list("GENDER", "DIS_AMI")) @@ -95,7 +96,7 @@ test_that("setup", { # Tests - Phase 2 # -context("ds.table::disc::tests::phase 2::table.assign=FALSE") +# context("ds.table::disc::tests::phase 2::table.assign=FALSE") test_that("table disclosure, table.assign=FALSE", { table.res <- ds.table(rvar='D$GENDER', cvar="D$DIS_AMI", table.assign=FALSE, newobj="new_table3") @@ -108,7 +109,7 @@ test_that("table disclosure, table.assign=FALSE", { expect_equal(table.res$error.message$sim3, "Failed: at least one cell has a non-zero count less than nfilter.tab i.e. 3", fixed = TRUE) }) -context("ds.table::disc::tests::phase 2::table.assign=TRUE") +# context("ds.table::disc::tests::phase 2::table.assign=TRUE") test_that("table disclosure, table.assign=TRUE", { table.res <- ds.table(rvar='D$GENDER', cvar="D$DIS_AMI", table.assign=TRUE, newobj="new_table4") @@ -119,7 +120,7 @@ test_that("table disclosure, table.assign=TRUE", { # Shutdown - Phase 2 # -context("ds.table::disc::shutdown::phase 2") +# context("ds.table::disc::shutdown::phase 2") test_that("setup", { ds_expect_variables(c("D", "new_table4")) @@ -131,4 +132,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.table::disc::done") +# context("ds.table::disc::done") diff --git a/tests/testthat/test-disc-ds.var.R b/tests/testthat/test-disc-ds.var.R index 08a445b92..39d6a506b 100644 --- a/tests/testthat/test-disc-ds.var.R +++ b/tests/testthat/test-disc-ds.var.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. @@ -18,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) # Tests # -context("ds.var::disc::type=both") +# context("ds.var::disc::type=both") test_that("var values [both]", { # myvectors <- c("D$LAB_TSC", "D$LAB_TRIG") # ds.dataFrame(x=myvectors, newobj="unsubset_df") diff --git a/tests/testthat/test-discctrl-ds.Boole.R b/tests/testthat/test-discctrl-ds.Boole.R index 80a5dc3d2..29591402e 100644 --- a/tests/testthat/test-discctrl-ds.Boole.R +++ b/tests/testthat/test-discctrl-ds.Boole.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.Boole::discctrl::setup") +# context("ds.Boole::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.Boole::discctrl") +# context("ds.Boole::discctrl") test_that("simple rep", { expect_error(ds.Boole("D$LAB_TSC", "D$LAB_TRIG", "=="), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -43,7 +43,7 @@ test_that("simple rep", { # Done # -context("ds.Boole::discctrl::shutdown") +# context("ds.Boole::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.Boole::discctrl::done") +# context("ds.Boole::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.c.R b/tests/testthat/test-discctrl-ds.c.R index da4a0caa6..e4bfb577e 100644 --- a/tests/testthat/test-discctrl-ds.c.R +++ b/tests/testthat/test-discctrl-ds.c.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("ds.c::discctrl::setup") +# context("ds.c::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.c::discctrl") +# context("ds.c::discctrl") test_that("simple c", { expect_error(ds.c("D$GENDER"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.c::discctrl::shutdown") +# context("ds.c::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.c::discctrl::done") +# context("ds.c::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.cbind.R b/tests/testthat/test-discctrl-ds.cbind.R index a829185e6..b1b3b79c2 100644 --- a/tests/testthat/test-discctrl-ds.cbind.R +++ b/tests/testthat/test-discctrl-ds.cbind.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.cbind::discctrl::setup") +# context("ds.cbind::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.cbind::discctrl") +# context("ds.cbind::discctrl") test_that("simple c", { expect_error(ds.cbind(x="D", DataSHIELD.checks=TRUE, datasources = ds.test_env$connections[1]), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -38,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.cbind::discctrl::shutdown") +# context("ds.cbind::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -46,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.cbind::discctrl::done") +# context("ds.cbind::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dataFrame.R b/tests/testthat/test-discctrl-ds.dataFrame.R index fe153c0e0..fedde1566 100644 --- a/tests/testthat/test-discctrl-ds.dataFrame.R +++ b/tests/testthat/test-discctrl-ds.dataFrame.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("ds.dataFrame::discctrl::setup") +# context("ds.dataFrame::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dataFrame::discctrl") +# context("ds.dataFrame::discctrl") test_that("simple c", { ds.assign('D$LAB_TSC', 'LAB_TSC') ds.assign('D$LAB_HDL', 'LAB_HDL') @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.dataFrame::discctrl::shutdown") +# context("ds.dataFrame::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TSC", "LAB_HDL")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrame::discctrl::done") +# context("ds.dataFrame::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dataFrameSort.R b/tests/testthat/test-discctrl-ds.dataFrameSort.R index 027c5d8ec..e85a55bd2 100644 --- a/tests/testthat/test-discctrl-ds.dataFrameSort.R +++ b/tests/testthat/test-discctrl-ds.dataFrameSort.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("ds.dataFrameSort::discctrl::setup") +# context("ds.dataFrameSort::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dataFrameSort::discctrl") +# context("ds.dataFrameSort::discctrl") test_that("simple c", { expect_error(ds.dataFrameSort(df.name="D", sort.key.name="PM_BMI_CATEGORICAL", newobj="sorted_df"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.dataFrameSort::discctrl::shutdown") +# context("ds.dataFrameSort::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrameSort::discctrl::done") +# context("ds.dataFrameSort::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dataFrameSubset.R b/tests/testthat/test-discctrl-ds.dataFrameSubset.R index c43d0c800..155313cba 100644 --- a/tests/testthat/test-discctrl-ds.dataFrameSubset.R +++ b/tests/testthat/test-discctrl-ds.dataFrameSubset.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("ds.dataFrameSubset::discctrl::setup") +# context("ds.dataFrameSubset::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dataFrameSubset::discctrl") +# context("ds.dataFrameSubset::discctrl") test_that("simple c", { expect_error(ds.dataFrameSubset(df.name="D", V1.name="D$LAB_TSC", V2.name="D$LAB_HDL", Boolean.operator="!=", newobj="subset_df"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.dataFrameSubset::discctrl::shutdown") +# context("ds.dataFrameSubset::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrameSubset::discctrl::done") +# context("ds.dataFrameSubset::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.dmtC2S.R b/tests/testthat/test-discctrl-ds.dmtC2S.R index fb2099a72..95af08e9c 100644 --- a/tests/testthat/test-discctrl-ds.dmtC2S.R +++ b/tests/testthat/test-discctrl-ds.dmtC2S.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("ds.dmtC2S::discctrl::setup") +# context("ds.dmtC2S::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.dmtC2S::discctrl") +# context("ds.dmtC2S::discctrl") test_that("simple dmtC2S", { a <- data.frame(c(1, 2)) b <- data.frame(c(2, 3)) @@ -46,7 +47,7 @@ test_that("simple dmtC2S", { # Done # -context("ds.dmtC2S::discctrl::shutdown") +# context("ds.dmtC2S::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -54,4 +55,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dmtC2S::discctrl::done") +# context("ds.dmtC2S::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.levels.R b/tests/testthat/test-discctrl-ds.levels.R index 05325f543..5690859f5 100644 --- a/tests/testthat/test-discctrl-ds.levels.R +++ b/tests/testthat/test-discctrl-ds.levels.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("ds.levels::discctrl::setup") +# context("ds.levels::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.levels::discctrl") +# context("ds.levels::discctrl") test_that("simple levels", { expect_error(ds.levels("D$GENDER"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple levels", { # Done # -context("ds.levels::discctrl::shutdown") +# context("ds.levels::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.levels::discctrl::done") +# context("ds.levels::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.ns.R b/tests/testthat/test-discctrl-ds.ns.R index c7c4a43df..8f57c17d2 100644 --- a/tests/testthat/test-discctrl-ds.ns.R +++ b/tests/testthat/test-discctrl-ds.ns.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -13,7 +13,7 @@ # Set up # -context("ds.ns::discctrl::setup") +# context("ds.ns::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.ns::discctrl") +# context("ds.ns::discctrl") test_that("ns", { expect_error(ds.ns(x="D$PM_BMI_CONTINUOUS", knots=c(8,9,10,12,25,35), newobj="nsDS", datasources=ds.test_env$connections), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -43,7 +43,7 @@ test_that("ns", { # Done # -context("ds.ns::discctrl::shutdown") +# context("ds.ns::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.ns::discctrl::done") +# context("ds.ns::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rBinom.R b/tests/testthat/test-discctrl-ds.rBinom.R index 19e2318ac..f8bc70d77 100644 --- a/tests/testthat/test-discctrl-ds.rBinom.R +++ b/tests/testthat/test-discctrl-ds.rBinom.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.rBinom::discctrl::setup") +# context("ds.rBinom::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rBinom::discctrl") +# context("ds.rBinom::discctrl") test_that("simple c", { expect_error(ds.rBinom(samp.size = 50, size = 50, prob = 0.25, newobj = "binom_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rBinom::discctrl::shutdown") +# context("ds.rBinom::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rBinom::discctrl::done") +# context("ds.rBinom::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rNorm.R b/tests/testthat/test-discctrl-ds.rNorm.R index 997e3fadb..153d84e03 100644 --- a/tests/testthat/test-discctrl-ds.rNorm.R +++ b/tests/testthat/test-discctrl-ds.rNorm.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.rNorm::discctrl::setup") +# context("ds.rNorm::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rNorm::discctrl") +# context("ds.rNorm::discctrl") test_that("simple c", { expect_error(ds.rNorm(samp.size = 50, mean = 10, sd = 5, newobj = "norm_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rNorm::discctrl::shutdown") +# context("ds.rNorm::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rNorm::discctrl::done") +# context("ds.rNorm::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rPois.R b/tests/testthat/test-discctrl-ds.rPois.R index 58b0667a0..b0176cedc 100644 --- a/tests/testthat/test-discctrl-ds.rPois.R +++ b/tests/testthat/test-discctrl-ds.rPois.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.rPois::discctrl::setup") +# context("ds.rPois::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rPois::discctrl") +# context("ds.rPois::discctrl") test_that("simple c", { expect_error(ds.rPois(samp.size = 50, lambda = 1, newobj = "pois_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rPois::discctrl::shutdown") +# context("ds.rPois::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rPois::discctrl::done") +# context("ds.rPois::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rUnif.R b/tests/testthat/test-discctrl-ds.rUnif.R index f2fd5e476..7327f366f 100644 --- a/tests/testthat/test-discctrl-ds.rUnif.R +++ b/tests/testthat/test-discctrl-ds.rUnif.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.rUnif::discctrl::setup") +# context("ds.rUnif::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rUnif::discctrl") +# context("ds.rUnif::discctrl") test_that("simple c", { expect_error(ds.rUnif(samp.size = 50, min = 0, max = 1, newobj = "unif_dist", seed.as.integer = 27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.rUnif::discctrl::shutdown") +# context("ds.rUnif::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rUnif::discctrl::done") +# context("ds.rUnif::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rbind.R b/tests/testthat/test-discctrl-ds.rbind.R index 28d3c0306..b80362070 100644 --- a/tests/testthat/test-discctrl-ds.rbind.R +++ b/tests/testthat/test-discctrl-ds.rbind.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("ds.rbind::discctrl::setup") +# context("ds.rbind::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rbind::discctrl") +# context("ds.rbind::discctrl") test_that("simple c", { expect_error(ds.rbind(c("D$survtime", "D$time.id", "D$female", "D$age.60"), newobj="rbind_newobj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.rbind::discctrl::shutdown") +# context("ds.rbind::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rbind::discctrl::done") +# context("ds.rbind::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.reShape.R b/tests/testthat/test-discctrl-ds.reShape.R index 65f68eb6d..ec759b697 100644 --- a/tests/testthat/test-discctrl-ds.reShape.R +++ b/tests/testthat/test-discctrl-ds.reShape.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("ds.reShape::discctrl::setup") +# context("ds.reShape::discctrl::setup") connect.studies.dataset.survival(list("id", "study.id", "time.id", "cens", "age.60", "female")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.reShape::discctrl") +# context("ds.reShape::discctrl") test_that("simple reShape", { expect_error(ds.reShape(data.name="D", v.names="age.60", timevar.name="time.id", idvar.name="id", direction="wide", newobj="reshape1_obj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple reShape", { # Done # -context("ds.reShape::discctrl::shutdown") +# context("ds.reShape::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.reShape::discctrl::done") +# context("ds.reShape::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.recodeLevels.R b/tests/testthat/test-discctrl-ds.recodeLevels.R index 9f4ab0ca9..39551aa15 100644 --- a/tests/testthat/test-discctrl-ds.recodeLevels.R +++ b/tests/testthat/test-discctrl-ds.recodeLevels.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("ds.recodeLevels::discctrl::setup") +# context("ds.recodeLevels::discctrl::setup") connect.studies.dataset.cnsim(list("PM_BMI_CATEGORICAL")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.recodeLevels::discctrl") +# context("ds.recodeLevels::discctrl") test_that("simple recodeLevels", { expect_error(expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL', newCategories=c('normal', 'overweight', 'obesity'), newobj='bmi_new'), "", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple recodeLevels", { # Done # -context("ds.recodeLevels::discctrl::shutdown") +# context("ds.recodeLevels::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeLevels::discctrl::done") +# context("ds.recodeLevels::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.recodeValues.R b/tests/testthat/test-discctrl-ds.recodeValues.R index 71580510c..1bd6aa93e 100644 --- a/tests/testthat/test-discctrl-ds.recodeValues.R +++ b/tests/testthat/test-discctrl-ds.recodeValues.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("ds.rep::discctrl::setup") +# context("ds.rep::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rep::discctrl") +# context("ds.rep::discctrl") test_that("simple recodeValues", { expect_error(ds.recodeValues("D$survtime", values2replace.vector=c(0,1), new.values.vector=c(-10,10), newobj="recodevalues_newobj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple recodeValues", { # Done # -context("ds.rep::discctrl::shutdown") +# context("ds.rep::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rep::discctrl::done") +# context("ds.rep::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.rep.R b/tests/testthat/test-discctrl-ds.rep.R index feeb56c97..4828cc8ef 100644 --- a/tests/testthat/test-discctrl-ds.rep.R +++ b/tests/testthat/test-discctrl-ds.rep.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::discctrl::setup") +# context("ds.rep::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.rep::discctrl") +# context("ds.rep::discctrl") test_that("simple rep", { expect_error(ds.rep("D$survtime"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple rep", { # Done # -context("ds.rep::discctrl::shutdown") +# context("ds.rep::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rep::discctrl::done") +# context("ds.rep::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.sample.R b/tests/testthat/test-discctrl-ds.sample.R index 0991669ff..863112a49 100644 --- a/tests/testthat/test-discctrl-ds.sample.R +++ b/tests/testthat/test-discctrl-ds.sample.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.sample::discctrl::setup") +# context("ds.sample::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.sample::discctrl") +# context("ds.sample::discctrl") test_that("simple c", { expect_error(ds.sample(x="D", size=20, seed.as.integer=27), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple c", { # Done # -context("ds.sample::discctrl::shutdown") +# context("ds.sample::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.sample::discctrl::done") +# context("ds.sample::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.seq.R b/tests/testthat/test-discctrl-ds.seq.R index 5045b06ae..a74ba73a7 100644 --- a/tests/testthat/test-discctrl-ds.seq.R +++ b/tests/testthat/test-discctrl-ds.seq.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("ds.seq::discctrl::setup") +# context("ds.seq::discctrl::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.seq::discctrl") +# context("ds.seq::discctrl") test_that("simple rep", { expect_error(ds.seq(FROM.value.char="1", BY.value.char="1", LENGTH.OUT.value.char="10", ALONG.WITH.name=NULL, newobj="obj1"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple rep", { # Done # -context("ds.seq::discctrl::shutdown") +# context("ds.seq::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.seq::discctrl::done") +# context("ds.seq::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.setSeed.R b/tests/testthat/test-discctrl-ds.setSeed.R index 351859c29..f32371b6b 100644 --- a/tests/testthat/test-discctrl-ds.setSeed.R +++ b/tests/testthat/test-discctrl-ds.setSeed.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.setSeed::discctrl::setup") +# context("ds.setSeed::discctrl::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.setSeed::discctrl") +# context("ds.setSeed::discctrl") test_that("simple c", { expect_error(ds.setSeed(4321), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -43,7 +43,7 @@ test_that("simple c", { # Done # -context("ds.setSeed::discctrl::shutdown") +# context("ds.setSeed::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.setSeed::discctrl::done") +# context("ds.setSeed::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.subset.R b/tests/testthat/test-discctrl-ds.subset.R index 6b99c7c83..6da2146d5 100644 --- a/tests/testthat/test-discctrl-ds.subset.R +++ b/tests/testthat/test-discctrl-ds.subset.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.subset::discctrl::setup") +# context("ds.subset::discctrl::setup") connect.studies.dataset.cnsim(list("DIS_DIAB","PM_BMI_CONTINUOUS","LAB_HDL", "GENDER")) @@ -24,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.subset::discctrl") +# context("ds.subset::discctrl") test_that("simple subset", { expect_error(expect_warning(ds.subset(datasources=ds.test_env$connections, subset='subD', x='D', rows=c(1:50), cols=c(1,2)), "", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -39,7 +39,7 @@ test_that("simple subset", { # Done # -context("ds.subset::discctrl::shutdown") +# context("ds.subset::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +47,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subset::discctrl::done") +# context("ds.subset::discctrl::done") diff --git a/tests/testthat/test-discctrl-ds.subsetByClass.R b/tests/testthat/test-discctrl-ds.subsetByClass.R index 414efb4d5..a767cd546 100644 --- a/tests/testthat/test-discctrl-ds.subsetByClass.R +++ b/tests/testthat/test-discctrl-ds.subsetByClass.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("ds.subsetByClass::discctrl::setup") +# context("ds.subsetByClass::discctrl::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.subsetByClass::discctrl") +# context("ds.subsetByClass::discctrl") test_that("simple subsetByClass", { expect_error(expect_warning(ds.subsetByClass(x='D', subsets='subclasses1'), "", fixed = TRUE), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -42,7 +43,7 @@ test_that("simple subsetByClass", { # Done # -context("ds.subsetByClass::discctrl::shutdown") +# context("ds.subsetByClass::discctrl::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subsetByClass::discctrl::done") +# context("ds.subsetByClass::discctrl::done") diff --git a/tests/testthat/test-expt-ds.dataFrame.R b/tests/testthat/test-expt-ds.dataFrame.R index 0ec01ef2b..3660038c8 100644 --- a/tests/testthat/test-expt-ds.dataFrame.R +++ b/tests/testthat/test-expt-ds.dataFrame.R @@ -1,9 +1,20 @@ -context('ds.dataFrame::expt::setup') +#------------------------------------------------------------------------------- +# 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. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + +# context('ds.dataFrame::expt::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.data.frame.R') -context('ds.dataFrame::expt::one_column::single') +# context('ds.dataFrame::expt::one_column::single') test_that('numeric data', { connect.dataset.2() @@ -17,7 +28,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$NEGATIVE_INTEGER'),'integer_7_df') }) -context('ds.dataFrame::expt::several_columns::single') +# context('ds.dataFrame::expt::several_columns::single') test_that('numeric data', { connect.dataset.2() @@ -25,7 +36,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$INTEGER','D$NON_NEGATIVE_INTEGER','D$POSITIVE_INTEGER','D$NEGATIVE_INTEGER'),'integer_9_df') }) -context('ds.dataFrame::expt::one_column::multiple') +# context('ds.dataFrame::expt::one_column::multiple') test_that('numeric data', { connect.all.datasets() @@ -39,7 +50,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$NEGATIVE_INTEGER'),'integer_16_df') }) -context('ds.dataFrame::expt::several_columns::single') +# context('ds.dataFrame::expt::several_columns::single') test_that('numeric data', { connect.all.datasets() @@ -47,7 +58,7 @@ test_that('numeric data', .test.data.frame.creation(c('D$INTEGER','D$NON_NEGATIVE_INTEGER','D$POSITIVE_INTEGER','D$NEGATIVE_INTEGER'),'integer_17_df') }) -context('ds.dataFrame::expt::one_column_from_objects::single') +# context('ds.dataFrame::expt::one_column_from_objects::single') test_that('numeric data', { connect.dataset.2() @@ -61,7 +72,7 @@ test_that('numeric data', .test.data.frame.from.objects('D$NEGATIVE_INTEGER','numeric_created','numeric_27_df') }) -context('ds.dataFrame::expt::object::multiple') +# context('ds.dataFrame::expt::object::multiple') test_that('numeric data', { connect.all.datasets() @@ -75,14 +86,14 @@ test_that('numeric data', .test.data.frame.from.objects('D$NEGATIVE_INTEGER','numeric_created','numeric_35_df') }) -context('ds.dataFrame::expt::several_objects::multiple') +# context('ds.dataFrame::expt::several_objects::multiple') test_that('several objects', { connect.all.datasets() .test.data.frame.from.different.objects('multiple_df') }) -context('ds.dataFrame::expt::non_numeric::multiple') +# context('ds.dataFrame::expt::non_numeric::multiple') test_that("non_numeric", { connect.all.datasets() @@ -93,7 +104,7 @@ test_that("non_numeric", .test.data.frame.from.objects('D$LOGICAL','boolean_created' ,'boolean_df') }) -context('ds.dataFrame::expt::non_numeric::multiple') +# context('ds.dataFrame::expt::non_numeric::multiple') { connect.dataset.2() .test.data.frame.creation(c('D$CHARACTER'),'character_df') @@ -103,6 +114,6 @@ context('ds.dataFrame::expt::non_numeric::multiple') .test.data.frame.from.objects('D$LOGICAL','boolean_created' ,'boolean_df') } -context('ds.dataFrame::expt::shutdown') +# context('ds.dataFrame::expt::shutdown') -context('ds.dataFrame::expt::done') +# context('ds.dataFrame::expt::done') diff --git a/tests/testthat/test-expt-ds.glmerSLMA.R b/tests/testthat/test-expt-ds.glmerSLMA.R index 0ce25e862..8c6fe40bc 100644 --- a/tests/testthat/test-expt-ds.glmerSLMA.R +++ b/tests/testthat/test-expt-ds.glmerSLMA.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("ds.glmerSLMA::expt::setup") +# context("ds.glmerSLMA::expt::setup") #source("connection_to_datasets/init_all_datasets.R") connect.studies.dataset.cluster.int(list('idChild','idSurgery','trtGrp','s0','nDoctors', 'idDoctor','c0','nPatients','Male','age','BMI', @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.glmerSLMA::expt::int::multiple") +# context("ds.glmerSLMA::expt::int::multiple") test_that("linear mixed model with 2 levels of hierarchy", { @@ -76,7 +77,7 @@ test_that("linear mixed model with 2 levels of hierarchy", # Shutdown # -context("ds.lmerSLMA::expt::shutdown") +# context("ds.lmerSLMA::expt::shutdown") disconnect.studies.dataset.cluster.int() @@ -84,4 +85,4 @@ disconnect.studies.dataset.cluster.int() # Done # -context("ds.lmerSLMA::expt::done") +# context("ds.lmerSLMA::expt::done") diff --git a/tests/testthat/test-expt-ds.lmerSLMA.R b/tests/testthat/test-expt-ds.lmerSLMA.R index 271381c6a..703a589dd 100644 --- a/tests/testthat/test-expt-ds.lmerSLMA.R +++ b/tests/testthat/test-expt-ds.lmerSLMA.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("ds.lmerSLMA::expt::setup") +# context("ds.lmerSLMA::expt::setup") #source("connection_to_datasets/init_all_datasets.R") connect.studies.dataset.cluster.int(list('idChild','idSurgery','trtGrp','s0','nDoctors', 'idDoctor','c0','nPatients','Male','age','BMI', @@ -27,7 +28,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::expt::int::multiple") +# context("ds.lmerSLMA::expt::int::multiple") test_that("linear mixed model with 2 levels of hierarchy", { @@ -79,4 +80,4 @@ test_that("linear mixed model with 2 levels of hierarchy", disconnect.studies.dataset.cluster.int() -context("ds.lmerSLMA::expt::done") +# context("ds.lmerSLMA::expt::done") diff --git a/tests/testthat/test-expt-ds.mean.R b/tests/testthat/test-expt-ds.mean.R index 8c6d6b44a..782a4acbe 100644 --- a/tests/testthat/test-expt-ds.mean.R +++ b/tests/testthat/test-expt-ds.mean.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. @@ -14,7 +15,7 @@ source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.mean.R") -context("ds.mean::expt::combine::multiple") +# context("ds.mean::expt::combine::multiple") test_that("combined data set", { connect.all.datasets() @@ -29,7 +30,7 @@ test_that("combined data set", .test.mean.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::split::multiple") +# context("ds.mean::expt::split::multiple") test_that("split data set", { connect.all.datasets() @@ -44,7 +45,7 @@ test_that("split data set", .test.mean.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::single") +# context("ds.mean::expt::single") test_that("combined data set", { connect.dataset.1() @@ -58,7 +59,7 @@ test_that("combined data set", .test.mean.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::large_values::single") +# context("ds.mean::expt::large_values::single") test_that("combined data set", { connect.dataset.1() @@ -72,7 +73,7 @@ test_that("combined data set", .test.mean.large('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC']) }) -context("ds.mean::expt::large_values::multiple") +# context("ds.mean::expt::large_values::multiple") test_that("combined data set", { connect.all.datasets() diff --git a/tests/testthat/test-expt-ds.reshape.R b/tests/testthat/test-expt-ds.reshape.R index 853d31af2..4e8f243b3 100644 --- a/tests/testthat/test-expt-ds.reshape.R +++ b/tests/testthat/test-expt-ds.reshape.R @@ -1,9 +1,20 @@ +#------------------------------------------------------------------------------- +# 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. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.reshape.R") source("definition_tests/def-assign-stats.R") -context("ds.reShape::expt::multiple") +# context("ds.reShape::expt::multiple") test_that("copy and transform", { init.testing.datasets() diff --git a/tests/testthat/test-expt-ds.skewness.R b/tests/testthat/test-expt-ds.skewness.R index d43bdce86..268ac3a13 100644 --- a/tests/testthat/test-expt-ds.skewness.R +++ b/tests/testthat/test-expt-ds.skewness.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. @@ -13,7 +14,7 @@ source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.skewness.R") -context("ds.skewness::expt::combine::multiple") +# context("ds.skewness::expt::combine::multiple") test_that("combined data set", { @@ -28,7 +29,7 @@ test_that("combined data set", .test.skewness.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC'], method = 1) }) -context("ds.skewness::expt::split::multiple") +# context("ds.skewness::expt::split::multiple") test_that("split data set", { connect.all.datasets() @@ -42,7 +43,7 @@ test_that("split data set", .test.skewness.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC'], method = 2) }) -context("ds.skewness::expt::single") +# context("ds.skewness::expt::single") test_that("combined data set", { connect.dataset.1() diff --git a/tests/testthat/test-expt-ds.var.R b/tests/testthat/test-expt-ds.var.R index e8a19fd4f..e4764f327 100644 --- a/tests/testthat/test-expt-ds.var.R +++ b/tests/testthat/test-expt-ds.var.R @@ -1,8 +1,19 @@ +#------------------------------------------------------------------------------- +# 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. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.var.R") -context("ds.var::expt::multiple") +# context("ds.var::expt::multiple") test_that("combined data set", { connect.all.datasets() @@ -16,7 +27,7 @@ test_that("combined data set", .test.var.combined('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC']) }) -context("ds.var::expt::single") +# context("ds.var::expt::single") test_that("split data set", { connect.all.datasets() @@ -30,7 +41,7 @@ test_that("split data set", .test.var.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC']) }) -context("ds.var::expt::large_values::multiple") +# context("ds.var::expt::large_values::multiple") test_that("large values", { connect.all.datasets() @@ -44,7 +55,7 @@ test_that("large values", .test.variance.large('D$NEGATIVE_NUMERIC',ds.test_env$local.values[,'NEGATIVE_NUMERIC']) }) -context("ds.var::expt::large_values::single") +# context("ds.var::expt::large_values::single") test_that("large values", { connect.dataset.1() @@ -58,4 +69,3 @@ test_that("large values", .test.variance.large('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC']) }) - diff --git a/tests/testthat/test-expt_bug-ds.asFactor.R b/tests/testthat/test-expt_bug-ds.asFactor.R index 16ca08534..b7f26c9ee 100644 --- a/tests/testthat/test-expt_bug-ds.asFactor.R +++ b/tests/testthat/test-expt_bug-ds.asFactor.R @@ -1,7 +1,17 @@ -source("definition_tests/def-ds.asFactor.R") +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- +source("definition_tests/def-ds.asFactor.R") -context("ds.asFactor::expt::multiple") +# context("ds.asFactor::expt::multiple") test_that("combined data set", { connect.all.datasets() @@ -16,7 +26,7 @@ test_that("combined data set", .test.find.factor('D$FACTOR_INTEGER', 'FACTOR_INT.f',ds.test_env$local.values,15) }) -context("ds.asFactor::expt::single") +# context("ds.asFactor::expt::single") test_that("single dataset ", { connect.dataset.1() diff --git a/tests/testthat/test-expt_bug-ds.dataFrameSort.R b/tests/testthat/test-expt_bug-ds.dataFrameSort.R index 7f4f065a3..522c28ca6 100644 --- a/tests/testthat/test-expt_bug-ds.dataFrameSort.R +++ b/tests/testthat/test-expt_bug-ds.dataFrameSort.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. @@ -8,12 +9,12 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -context('ds.dataFrameSort::expt::setup') +# context('ds.dataFrameSort::expt::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSort.R') -context("ds.dataFrameSort::expt::multiple::correct_parameter_class") +# context("ds.dataFrameSort::expt::multiple::correct_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -31,7 +32,7 @@ test_that('all datasets', .test.function.parameters("D","D$NUMERIC_ONE_CHANGE",TRUE,"alphabetic","server.data") .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::single::correct_parameter_class") +# context("ds.dataFrameSort::expt::single::correct_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -49,7 +50,7 @@ test_that('dataset 2', .test.function.parameters("D","D$NUMERIC_ONE_CHANGE",TRUE,"alphabetic","server.data") .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::multiple::incorrect_parameter_class") +# context("ds.dataFrameSort::expt::multiple::incorrect_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -65,7 +66,7 @@ test_that('all datasets', .test.function.parameters("D","D$NUMERIC_ONE_CHANGE",TRUE,"alphabetic",23) .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::single::incorrect_parameter_class") +# context("ds.dataFrameSort::expt::single::incorrect_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -82,7 +83,7 @@ test_that('dataset 2', .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::multiple::df::creation") +# context("ds.dataFrameSort::expt::multiple::df::creation") test_that('all datasets', { connect.all.datasets() @@ -98,7 +99,7 @@ test_that('all datasets', .test.data.frame.creation("D","NUMERIC_ONE_CHANGE",TRUE,"numeric","server.data") .test.data.frame.creation("D","INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt::single::df::creation") +# context("ds.dataFrameSort::expt::single::df::creation") test_that('dataset 3', { connect.dataset.3() @@ -114,7 +115,7 @@ test_that('dataset 3', .test.data.frame.creation("D","NUMERIC_ONE_CHANGE",TRUE,"numeric","server.data") .test.data.frame.creation("D","INTEGER_ONE_CHANGE",FALSE,"alphabetic","server.data") }) -context("ds.dataFrameSort::expt::multiple::numeric::ascending") +# context("ds.dataFrameSort::expt::multiple::numeric::ascending") test_that('all datasets', { connect.all.datasets() @@ -140,7 +141,7 @@ test_that('all datasets', }) -context("ds.dataFrameSort::expt::single::numeric::ascending") +# context("ds.dataFrameSort::expt::single::numeric::ascending") test_that('dataset 1', { connect.dataset.1() @@ -166,7 +167,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSort::expt::multiple::numeric::descending") +# context("ds.dataFrameSort::expt::multiple::numeric::descending") test_that('all datasets', { connect.all.datasets() @@ -192,7 +193,7 @@ test_that('all datasets', }) -context("ds.dataFrameSort::expt::single::numeric::descending") +# context("ds.dataFrameSort::expt::single::numeric::descending") test_that('dataset 1', { connect.dataset.1() @@ -220,7 +221,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSort::expt::multiple::alphabetic::ascending") +# context("ds.dataFrameSort::expt::multiple::alphabetic::ascending") test_that('all datasets', { connect.all.datasets() @@ -246,7 +247,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","FACTOR_CHARACTER",FALSE,"alphabetic","server.data",local.df.list) .test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",local.df.list) }) -context("ds.dataFrameSort::expt::single::alphabetic::ascending") +# context("ds.dataFrameSort::expt::single::alphabetic::ascending") test_that('dataset 2', { connect.dataset.2() @@ -272,7 +273,7 @@ test_that('dataset 2', #.test.data.frame.sorting("D","FACTOR_CHARACTER",FALSE,"alphabetic","server.data",local.df.list) .test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",local.df.list) }) -context("ds.dataFrameSort::expt::multiple::alphabetic::descending") +# context("ds.dataFrameSort::expt::multiple::alphabetic::descending") test_that('all datasets', { connect.all.datasets() @@ -296,7 +297,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","FACTOR_CHARACTER",TRUE,"alphabetic","server.data",local.df.list) .test.data.frame.sorting("D","CHARACTER",TRUE,"alphabetic","server.data",local.df.list) }) -context("ds.dataFrameSort::expt::single::alphabetic::descending") +# context("ds.dataFrameSort::expt::single::alphabetic::descending") test_that('dataset 3', { connect.dataset.3() @@ -322,7 +323,7 @@ test_that('dataset 3', }) -context('ds.dataFrameSort::expt::shutdown') +# context('ds.dataFrameSort::expt::shutdown') -context('ds.dataFrameSort::expt::done') +# context('ds.dataFrameSort::expt::done') diff --git a/tests/testthat/test-expt_bug-ds.make.R b/tests/testthat/test-expt_bug-ds.make.R index 2b5005d03..1bcf320cc 100644 --- a/tests/testthat/test-expt_bug-ds.make.R +++ b/tests/testthat/test-expt_bug-ds.make.R @@ -1,9 +1,20 @@ +#------------------------------------------------------------------------------- +# 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. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.make.R") source("definition_tests/def-assign-stats.R") -context("ds.make::expt::copy_transform:single") +# context("ds.make::expt::copy_transform:single") test_that("copy and transform", { connect.dataset.1() @@ -20,7 +31,7 @@ test_that("copy and transform", -context("ds.make::expt::copy_data::single") +# context("ds.make::expt::copy_data::single") test_that("copy data without any changes applied", { connect.dataset.1() @@ -35,7 +46,7 @@ test_that("copy data without any changes applied", .test.copy.data('D$FACTOR_INTEGER','FACTOR_INTEGER_created',ds.test_env$local.values.1[,15]) }) -context("ds.make::expt::copy_data::multiple") +# context("ds.make::expt::copy_data::multiple") test_that("copy data without any changes applied", { connect.all.datasets() @@ -50,7 +61,7 @@ test_that("copy data without any changes applied", .test.copy.data('D$FACTOR_INTEGER','FACTOR_INTEGER_created',ds.test_env$local.values[,15]) }) -context("ds.make::expt::sum_of_two_vectors::single") +# context("ds.make::expt::sum_of_two_vectors::single") test_that("apply the the sum some vectors", { connect.dataset.1() @@ -82,7 +93,7 @@ test_that("apply the the sum some vectors", }) -context("ds.make::expt::sum_of_two_vectors::multiple") +# context("ds.make::expt::sum_of_two_vectors::multiple") test_that("add some vectors", { connect.all.datasets() @@ -111,7 +122,7 @@ test_that("add some vectors", .test.operation.vectors('D$NUMERIC','D$NON_NEGATIVE_NUMERIC','NUMERIC_created',"+",result.local = .add.vectors(ds.test_env$local.values[,10],ds.test_env$local.values[,11])) }) -context("ds.make::expt::product_of_two_vectors::single") +# context("ds.make::expt::product_of_two_vectors::single") test_that("multiply two vectors", { connect.dataset.1() @@ -144,7 +155,7 @@ test_that("multiply two vectors", -context("ds.make::expt::product_of_two_vectors::multiple") +# context("ds.make::expt::product_of_two_vectors::multiple") test_that("multiply two vectors", { connect.all.datasets() @@ -173,7 +184,7 @@ test_that("multiply two vectors", .test.operation.vectors('D$NUMERIC','D$NON_NEGATIVE_NUMERIC','NUMERIC_created',"*",result.local = .mult.vectors(ds.test_env$local.values[,10],ds.test_env$local.values[,11])) }) -context("ds.make::expt::division_of_two_vectors::multiple") +# context("ds.make::expt::division_of_two_vectors::multiple") test_that("divide two vectors", { connect.all.datasets() @@ -202,7 +213,7 @@ test_that("divide two vectors", }) -context("ds.make::expt::division_of_two_vectors::single") +# context("ds.make::expt::division_of_two_vectors::single") test_that("divide two vectors", { connect.dataset.1() @@ -231,7 +242,7 @@ test_that("divide two vectors", }) -context("ds.make::expt::substract_of_two_vectors::multiple") +# context("ds.make::expt::substract_of_two_vectors::multiple") test_that("substract two vectors", { connect.all.datasets() @@ -260,7 +271,7 @@ test_that("substract two vectors", }) -context("ds.make::expt::substract_of_two_vectors::single") +# context("ds.make::expt::substract_of_two_vectors::single") test_that("substract two vectors", { connect.dataset.1() @@ -289,7 +300,7 @@ test_that("substract two vectors", }) -context("ds.make::expt::sum_of_constant::single") +# context("ds.make::expt::sum_of_constant::single") test_that("apply the the sum a vector and a constant value", { connect.dataset.1() @@ -306,7 +317,7 @@ test_that("apply the the sum a vector and a constant value", }) -context("ds.make::expt::substract_of_constant::single") +# context("ds.make::expt::substract_of_constant::single") test_that("substract a constant value to all the values of a vector", { connect.dataset.1() @@ -324,7 +335,7 @@ test_that("substract a constant value to all the values of a vector", }) -context("ds.make::expt::divide_of_constant::single") +# context("ds.make::expt::divide_of_constant::single") test_that("divide a constant value to all the values of a vector", { connect.dataset.1() @@ -341,7 +352,7 @@ test_that("divide a constant value to all the values of a vector", }) -context("ds.make::expt::multiply_of_constant::single") +# context("ds.make::expt::multiply_of_constant::single") test_that("multiply a constant value to all the values of a vector", { connect.dataset.1() @@ -359,7 +370,7 @@ test_that("multiply a constant value to all the values of a vector", }) -context("ds.make::expt::sum_of_constant::multiple") +# context("ds.make::expt::sum_of_constant::multiple") test_that("apply the the sum a vector and a constant value", { connect.all.datasets() @@ -376,7 +387,7 @@ test_that("apply the the sum a vector and a constant value", }) -context("ds.make::expt::substract_of_constant::multiple") +# context("ds.make::expt::substract_of_constant::multiple") test_that("substract a constant value to all the values of a vector", { connect.all.datasets() @@ -394,7 +405,7 @@ test_that("substract a constant value to all the values of a vector", }) -context("ds.make::expt::divide_of_constant::multiple") +# context("ds.make::expt::divide_of_constant::multiple") test_that("divide a constant value to all the values of a vector", { connect.all.datasets() @@ -411,7 +422,7 @@ test_that("divide a constant value to all the values of a vector", }) -context("ds.make::expt::multiply_of_constant::multiple") +# context("ds.make::expt::multiply_of_constant::multiple") test_that("multiply a constant value to all the values of a vector", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.rPois.R b/tests/testthat/test-expt_bug-ds.rPois.R index 5e2b808a6..41716ac90 100644 --- a/tests/testthat/test-expt_bug-ds.rPois.R +++ b/tests/testthat/test-expt_bug-ds.rPois.R @@ -1,8 +1,19 @@ +#------------------------------------------------------------------------------- +# 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. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.rPois.R") -context("ds.rPois::expt::no seeds::single") +# context("ds.rPois::expt::no seeds::single") test_that("Poisson without seeds", { connect.dataset.1() @@ -15,7 +26,7 @@ test_that("Poisson without seeds", }) -context("ds.rPois::expt::no seeds::multiple") +# context("ds.rPois::expt::no seeds::multiple") test_that("Poisson without seeds", { connect.all.datasets() @@ -29,7 +40,7 @@ test_that("Poisson without seeds", -context("ds.rPois::expt::with seeds::single") +# context("ds.rPois::expt::with seeds::single") test_that("Poisson with seeds", { @@ -44,7 +55,7 @@ test_that("Poisson with seeds", .test.basic.expectation.with.seeds(2^31,'poisson_dist_7') }) -context("ds.rPois::expt::with seeds::multiple") +# context("ds.rPois::expt::with seeds::multiple") test_that("Poisson with seeds", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.rUnif.R b/tests/testthat/test-expt_bug-ds.rUnif.R index 845d3fa0f..f026843c8 100644 --- a/tests/testthat/test-expt_bug-ds.rUnif.R +++ b/tests/testthat/test-expt_bug-ds.rUnif.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# 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. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.rUnif.R") -context("ds.rUnif::expt::no_seeds::single") +# context("ds.rUnif::expt::no_seeds::single") test_that("basic expectation", { connect.dataset.2() @@ -14,7 +25,7 @@ test_that("basic expectation", .test.basic.expectation(2^31-1,'uniform_dist_6') }) -context("ds.rUnif::expt::no_seeds::multiple") +# context("ds.rUnif::expt::no_seeds::multiple") test_that("basic expectation", { connect.all.datasets() @@ -27,7 +38,7 @@ test_that("basic expectation", .test.basic.expectation(2^31-1,'uniform_dist_6') }) -context("ds.rUnif::expt::seeds::single") +# context("ds.rUnif::expt::seeds::single") test_that("basic expectation", { connect.dataset.2() @@ -40,7 +51,7 @@ test_that("basic expectation", .test.basic.expectation.with.seeds(2^31-1,'uniform_dist_6') }) -context("ds.rUnif::expt::seeds::multiple") +# context("ds.rUnif::expt::seeds::multiple") test_that("basic expectation", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.recodeValues.R b/tests/testthat/test-expt_bug-ds.recodeValues.R index 4a35f9b27..4f6bf6599 100644 --- a/tests/testthat/test-expt_bug-ds.recodeValues.R +++ b/tests/testthat/test-expt_bug-ds.recodeValues.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# 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. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.recodeValues.R") -context("ds.recodeValues::expt::changes_applied::single::") +# context("ds.recodeValues::expt::changes_applied::single::") test_that("changes must be applied", { @@ -40,7 +51,7 @@ test_that("changes must be applied", }) -context("ds.recodeValues::expt::changes_applied::multiple") +# context("ds.recodeValues::expt::changes_applied::multiple") test_that("changes must be applied", { @@ -81,7 +92,7 @@ test_that("changes must be applied", - context("ds.recodeValues::expt::no_change_applied::single") + # context("ds.recodeValues::expt::no_change_applied::single") test_that("no_change_applied", { connect.dataset.1() @@ -129,7 +140,7 @@ test_that("changes must be applied", }) -context("ds.recodeValues::expt::no_change_applied::multiple") +# context("ds.recodeValues::expt::no_change_applied::multiple") test_that("no_change_applied", { connect.all.datasets() diff --git a/tests/testthat/test-expt_bug-ds.table.R b/tests/testthat/test-expt_bug-ds.table.R index 23844fdf6..1834fca0a 100644 --- a/tests/testthat/test-expt_bug-ds.table.R +++ b/tests/testthat/test-expt_bug-ds.table.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# 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. @@ -8,10 +9,10 @@ # along with this program. If not, see . #------------------------------------------------------------------------------- -context("ds.table::expt::setup") +# context("ds.table::expt::setup") connect.testing.group.dataset.1() -context("ds.table::expt::single") +# context("ds.table::expt::single") test_that("combined data set", { #PRW AND ALEX WILL WRITE SOME CONNECT AND DISCONNECT FUNCTIONS ONCE WE KNOW THE DATA ARE SUITABLE - TO DO IMPORTANT !!!!!!!! COMPLETELY INEFFICIENT AT THE MOMENT 17/2/2020 diff --git a/tests/testthat/test-expt_dgr-ds.dataFrameSort.R b/tests/testthat/test-expt_dgr-ds.dataFrameSort.R index 251170e72..9ff0bca2b 100644 --- a/tests/testthat/test-expt_dgr-ds.dataFrameSort.R +++ b/tests/testthat/test-expt_dgr-ds.dataFrameSort.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('ds.dataFrameSort::expt_dgr::setup') +# context('ds.dataFrameSort::expt_dgr::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSort.R') @@ -21,7 +22,7 @@ source('definition_tests/def-ds.dataFrameSort.R') # Tests # -context("ds.dataFrameSort::expt_dgr::multiple::correct_parameter_class") +# context("ds.dataFrameSort::expt_dgr::multiple::correct_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -40,7 +41,7 @@ test_that('all datasets', .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::single::correct_parameter_class") +# context("ds.dataFrameSort::expt_dgr::single::correct_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -59,7 +60,7 @@ test_that('dataset 2', .test.function.parameters("D","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::multiple::incorrect_parameter_class") +# context("ds.dataFrameSort::expt_dgr::multiple::incorrect_parameter_class") test_that('all datasets', { connect.all.datasets() @@ -76,7 +77,7 @@ test_that('all datasets', .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::single::incorrect_parameter_class") +# context("ds.dataFrameSort::expt_dgr::single::incorrect_parameter_class") test_that('dataset 2', { connect.dataset.2() @@ -93,7 +94,7 @@ test_that('dataset 2', .test.function.parameters("dataframe","D$INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::multiple::df::creation") +# context("ds.dataFrameSort::expt_dgr::multiple::df::creation") test_that('all datasets', { connect.all.datasets() @@ -110,7 +111,7 @@ test_that('all datasets', .test.data.frame.creation("D","INTEGER_ONE_CHANGE",TRUE,"numeric","server.data") }) -context("ds.dataFrameSort::expt_dgr::single::df::creation") +# context("ds.dataFrameSort::expt_dgr::single::df::creation") test_that('dataset 3', { connect.dataset.3() @@ -127,7 +128,7 @@ test_that('dataset 3', .test.data.frame.creation("D","INTEGER_ONE_CHANGE",FALSE,"alphabetic","server.data") }) -context("ds.dataFrameSort::expt_dgr::multiple::numeric::ascending") +# context("ds.dataFrameSort::expt_dgr::multiple::numeric::ascending") test_that('all datasets', { connect.all.datasets() @@ -148,7 +149,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","CHARACTER",FALSE,"numeric","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::single::numeric::ascending") +# context("ds.dataFrameSort::expt_dgr::single::numeric::ascending") test_that('dataset 1', { connect.dataset.1() @@ -169,7 +170,7 @@ test_that('dataset 1', #.test.data.frame.sorting("D","CHARACTER",FALSE,"numeric","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::multiple::numeric::descending") +# context("ds.dataFrameSort::expt_dgr::multiple::numeric::descending") test_that('all datasets', { connect.all.datasets() @@ -192,7 +193,7 @@ test_that('all datasets', }) -context("ds.dataFrameSort::expt_dgr::single::numeric::descending") +# context("ds.dataFrameSort::expt_dgr::single::numeric::descending") test_that('dataset 1', { connect.dataset.1() @@ -214,7 +215,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::ascending") +# context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::ascending") test_that('all datasets', { #connect.all.datasets() @@ -242,7 +243,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::single::alphabetic::ascending") +# context("ds.dataFrameSort::expt_dgr::single::alphabetic::ascending") test_that('dataset 2', { #connect.dataset.2() @@ -270,7 +271,7 @@ test_that('dataset 2', #.test.data.frame.sorting("D","CHARACTER",FALSE,"alphabetic","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::descending") +# context("ds.dataFrameSort::expt_dgr::multiple::alphabetic::descending") test_that('all datasets', { #connect.all.datasets() @@ -296,7 +297,7 @@ test_that('all datasets', #.test.data.frame.sorting("D","CHARACTER",TRUE,"alphabetic","server.data",all.local.values) }) -context("ds.dataFrameSort::expt_dgr::single::alphabetic::descending") +# context("ds.dataFrameSort::expt_dgr::single::alphabetic::descending") test_that('dataset 3', { #connect.dataset.3() @@ -326,10 +327,10 @@ test_that('dataset 3', # Shutdown # -context('ds.dataFrameSort::expt_dgr::shutdown') +# context('ds.dataFrameSort::expt_dgr::shutdown') # # Done # -context('ds.dataFrameSort::expt_dgr::done') +# context('ds.dataFrameSort::expt_dgr::done') diff --git a/tests/testthat/test-expt_dgr-ds.dataFrameSubset.R b/tests/testthat/test-expt_dgr-ds.dataFrameSubset.R index 222d41bd5..278403ec9 100644 --- a/tests/testthat/test-expt_dgr-ds.dataFrameSubset.R +++ b/tests/testthat/test-expt_dgr-ds.dataFrameSubset.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("ds.dataFrameSubset::expt_dgr::setup") +# context("ds.dataFrameSubset::expt_dgr::setup") source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.dataFrameSubset.R") @@ -21,7 +22,7 @@ source("definition_tests/def-ds.dataFrameSubset.R") # Tests # -context("ds.dataFrameSubset::expt_dgr::multiple::parameter_class") +# context("ds.dataFrameSubset::expt_dgr::multiple::parameter_class") test_that('all datasets', { connect.all.datasets() @@ -41,7 +42,7 @@ test_that('all datasets', }) -context("ds.dataFrameSubset::expt_dgr::single::parameter_class") +# context("ds.dataFrameSubset::expt_dgr::single::parameter_class") test_that('dataset 1', { connect.dataset.1() @@ -61,7 +62,7 @@ test_that('dataset 1', }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_columns") test_that('all datasets', { connect.all.datasets() @@ -73,7 +74,7 @@ test_that('all datasets', .test.data.frame.creation("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=","subset.server") }) -context("ds.dataFrameSubset::expt_dgr::single::all_columns") +# context("ds.dataFrameSubset::expt_dgr::single::all_columns") test_that('dataset 2', { connect.dataset.2() @@ -85,7 +86,7 @@ test_that('dataset 2', .test.data.frame.creation("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=","subset.server") }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_columns::subset_by_rows") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_columns::subset_by_rows") test_that("all datasets", { connect.all.datasets() @@ -104,7 +105,7 @@ test_that("all datasets", subset.by.rows("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::single::all_columns::subset_by_rows") +# context("ds.dataFrameSubset::expt_dgr::single::all_columns::subset_by_rows") test_that("dataset 3", { connect.dataset.3() @@ -123,7 +124,7 @@ test_that("dataset 3", subset.by.rows("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") test_that("all datasets", { connect.all.datasets() @@ -142,7 +143,7 @@ test_that("all datasets", subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") test_that("dataset 1", { connect.dataset.1() @@ -162,7 +163,7 @@ test_that("dataset 1", }) -context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::subset_by_rows_columns") test_that("all datasets", { connect.all.datasets() @@ -180,7 +181,7 @@ test_that("all datasets", subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",TRUE,"subset.server",local.df.list) subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") +# context("ds.dataFrameSubset::expt_dgr::single::subset_by_rows_columns") test_that("dataset 2", { connect.dataset.2() @@ -199,7 +200,7 @@ test_that("dataset 2", subset.by.rows.cols("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC",1:15,"<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") test_that("all datasets", { connect.all.datasets() local.df.list<-list(ds.test_env$local.values.1,ds.test_env$local.values.2,ds.test_env$local.values.3) @@ -211,7 +212,7 @@ test_that("all datasets", subset.by.cols("D","NON_NEGATIVE_NUMERIC",c(1:7,13:16),FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") +# context("ds.dataFrameSubset::expt_dgr::multiple::all_rows_subset_by_columns") test_that("dataset 3", { connect.dataset.3() local.df.list<-list(ds.test_env$local.values.3) diff --git a/tests/testthat/test-math-ds.mean.R b/tests/testthat/test-math-ds.mean.R index 601e6a502..4c2a15593 100644 --- a/tests/testthat/test-math-ds.mean.R +++ b/tests/testthat/test-math-ds.mean.R @@ -1,9 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.mean.R") - - -context("ds.mean::math::residual::multiple") +# context("ds.mean::math::residual::multiple") test_that("residual deviation tends to 0", { connect.all.datasets() @@ -27,7 +36,7 @@ test_that("residual deviation tends to 0", }) -context("ds.mean::math::residual::multiple") +# context("ds.mean::math::residual::multiple") test_that("residual deviation tends to 0", { connect.all.datasets() @@ -53,7 +62,7 @@ test_that("residual deviation tends to 0", }) -context("ds.mean::math::location_parameter::single") +# context("ds.mean::math::location_parameter::single") test_that("mean(X+a) - mean(X) = a", { connect.dataset.1() @@ -68,7 +77,7 @@ test_that("mean(X+a) - mean(X) = a", .test.location.parameter('D$NEGATIVE_NUMERIC') }) -context("ds.mean::math::location_parameter::multiple") +# context("ds.mean::math::location_parameter::multiple") test_that("mean(X+a) - mean(X) = a", { connect.all.datasets() @@ -86,7 +95,7 @@ test_that("mean(X+a) - mean(X) = a", -context("ds.mean::math::scale::multiple") +# context("ds.mean::math::scale::multiple") test_that("mean(X+a) / mean(X) = a", { connect.all.datasets() @@ -101,7 +110,7 @@ test_that("mean(X+a) / mean(X) = a", .test.scale('D$NEGATIVE_NUMERIC') }) -context("ds.mean::math::scale::single") +# context("ds.mean::math::scale::single") test_that("mean(X*a) / mean(X) = a", { connect.dataset.1() diff --git a/tests/testthat/test-math-ds.var.R b/tests/testthat/test-math-ds.var.R index 47a7270d7..e281c5d62 100644 --- a/tests/testthat/test-math-ds.var.R +++ b/tests/testthat/test-math-ds.var.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.var.R") -context("ds.var::math::positive_result::multiple") +# context("ds.var::math::positive_result::multiple") test_that("variance >=0", { connect.all.datasets() @@ -25,7 +36,7 @@ test_that("variance >=0", }) -context("ds.var::math::positive_result::single") +# context("ds.var::math::positive_result::single") test_that("variance >=0", { connect.dataset.1() @@ -49,7 +60,7 @@ test_that("variance >=0", }) -context("ds.var::math::square_root_std::single") +# context("ds.var::math::square_root_std::single") test_that("variance is to the power of 2 of the standard deviation", { connect.dataset.1() @@ -65,7 +76,7 @@ test_that("variance is to the power of 2 of the standard deviation", }) -context("ds.var::math::square_root_std::multiple") +# context("ds.var::math::square_root_std::multiple") test_that("variance is to the power of 2 of the standard deviation", { connect.all.datasets() @@ -88,7 +99,7 @@ test_that("variance is to the power of 2 of the standard deviation", .test.standard.dev.split('D$NEGATIVE_NUMERIC',ds.test_env$local.values.1[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.2[,'NEGATIVE_NUMERIC'],ds.test_env$local.values.3[,'NEGATIVE_NUMERIC']) }) -context("ds.var::math::location::parameter::single") +# context("ds.var::math::location::parameter::single") test_that("var (X+a) = Var(X)", { connect.dataset.1() @@ -102,7 +113,7 @@ test_that("var (X+a) = Var(X)", .test.location.parameter('D$NEGATIVE_NUMERIC') }) -context("ds.var::math::location::parameter::multiple") +# context("ds.var::math::location::parameter::multiple") test_that("var (X+a) = Var(X)", { connect.all.datasets() @@ -116,7 +127,7 @@ test_that("var (X+a) = Var(X)", .test.location.parameter('D$NEGATIVE_NUMERIC') }) -context("ds.var::math::scale::single") +# context("ds.var::math::scale::single") test_that("var (aX) = a^2Var(X)", { connect.dataset.1() @@ -130,7 +141,7 @@ test_that("var (aX) = a^2Var(X)", .test.scale('D$NEGATIVE_NUMERIC') }) -context("ds.var::math::scale::multiple") +# context("ds.var::math::scale::multiple") test_that("var (aX) = a^2Var(X)", { connect.all.datasets() @@ -143,5 +154,3 @@ test_that("var (aX) = a^2Var(X)", .test.scale('D$POSITIVE_NUMERIC') .test.scale('D$NEGATIVE_NUMERIC') }) - - diff --git a/tests/testthat/test-math_bug-ds.asFactor.R b/tests/testthat/test-math_bug-ds.asFactor.R index def587df6..cb44c2fa1 100644 --- a/tests/testthat/test-math_bug-ds.asFactor.R +++ b/tests/testthat/test-math_bug-ds.asFactor.R @@ -1,7 +1,19 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- +# + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.asFactor.R") -context("ds.asFactor::math::multiple") +# context("ds.asFactor::math::multiple") test_that("every factor should be unique", { connect.all.datasets() @@ -16,7 +28,7 @@ test_that("every factor should be unique", .test.uniqueness('D$FACTOR_INTEGER', 'FACTOR_INT.f') }) -context("ds.asFactor::math::multiple") +# context("ds.asFactor::math::multiple") test_that("every factor should be unique", { connect.dataset.1() diff --git a/tests/testthat/test-math_bug-ds.make.R b/tests/testthat/test-math_bug-ds.make.R index 4a5de5d98..2823af009 100644 --- a/tests/testthat/test-math_bug-ds.make.R +++ b/tests/testthat/test-math_bug-ds.make.R @@ -1,8 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.make.R") - -context("ds.make::math::transformation::multiple") +# context("ds.make::math::transformation::multiple") test_that("transformation", { connect.all.datasets() diff --git a/tests/testthat/test-math_bug-ds.rPois.R b/tests/testthat/test-math_bug-ds.rPois.R index 4aa6f803d..b920cfff0 100644 --- a/tests/testthat/test-math_bug-ds.rPois.R +++ b/tests/testthat/test-math_bug-ds.rPois.R @@ -1,9 +1,20 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.rPois.R") random.number <- as.integer(as.POSIXct(Sys.time(), "GMT")) -context("ds.rPois::math::lambda equal mean and var::single") +# context("ds.rPois::math::lambda equal mean and var::single") test_that("lamdba == mean and lambda == var", { connect.dataset.1() @@ -14,7 +25,7 @@ test_that("lamdba == mean and lambda == var", }) -context("ds.rPois::math::lambda equal mean and var::multiple") +# context("ds.rPois::math::lambda equal mean and var::multiple") test_that("lamdba == mean and lambda == var", { connect.all.datasets() @@ -25,7 +36,7 @@ test_that("lamdba == mean and lambda == var", }) -context("ds.rPois::math::distributions comparison::multiple") +# context("ds.rPois::math::distributions comparison::multiple") test_that("changes in distribution", { connect.all.datasets() @@ -37,7 +48,7 @@ test_that("changes in distribution", .test.dispersions.stats.diff.distribution(seed/1000, c(1900),seed,c(1100)) }) -context("ds.rPois::math::distributions comparison::single") +# context("ds.rPois::math::distributions comparison::single") test_that("changes in distribution", { connect.dataset.3() diff --git a/tests/testthat/test-math_bug-ds.rUnif.R b/tests/testthat/test-math_bug-ds.rUnif.R index 123314a9f..7ca2da888 100644 --- a/tests/testthat/test-math_bug-ds.rUnif.R +++ b/tests/testthat/test-math_bug-ds.rUnif.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. @@ -13,7 +14,7 @@ source("definition_tests/def-ds.rUnif.R") random.number <- as.integer(as.POSIXct(Sys.time(), "GMT")) -context("ds.rUnif::math::mean_variance::single") +# context("ds.rUnif::math::mean_variance::single") test_that("mean_variance", { connect.dataset.1() @@ -23,7 +24,7 @@ test_that("mean_variance", .test.range.values(-200,-100,"uniform_3",seed) }) -context("ds.rUnif::math::distributions comparison::single") +# context("ds.rUnif::math::distributions comparison::single") test_that("changes in distribution", { connect.dataset.3() @@ -37,7 +38,7 @@ test_that("changes in distribution", }) -context("ds.rUnif::math::distributions comparison::multiple") +# context("ds.rUnif::math::distributions comparison::multiple") test_that("changes in distribution", { connect.all.datasets() diff --git a/tests/testthat/test-math_bug-ds.recodeValues.R b/tests/testthat/test-math_bug-ds.recodeValues.R index f34df1ea3..b5e452398 100644 --- a/tests/testthat/test-math_bug-ds.recodeValues.R +++ b/tests/testthat/test-math_bug-ds.recodeValues.R @@ -1,8 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.recodeValues.R") - -context("ds.recodeValues::math::single") +# context("ds.recodeValues::math::single") test_that("difference", { connect.dataset.1() @@ -65,7 +75,7 @@ test_that("difference", -context("ds.recodeValues::math::multiple") +# context("ds.recodeValues::math::multiple") test_that("difference", { connect.all.datasets() diff --git a/tests/testthat/test-math_bug-ds.table.R b/tests/testthat/test-math_bug-ds.table.R index 4f221c647..db0bd51ee 100644 --- a/tests/testthat/test-math_bug-ds.table.R +++ b/tests/testthat/test-math_bug-ds.table.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. @@ -9,7 +10,7 @@ #------------------------------------------------------------------------------- -context("ds.table::math::row and col proportions::multiple") +# context("ds.table::math::row and col proportions::multiple") test_that("row and col proportions sum to 1", { diff --git a/tests/testthat/test-math_dgr-ds.dataFrameSort.R b/tests/testthat/test-math_dgr-ds.dataFrameSort.R index e7d68279a..21d166472 100644 --- a/tests/testthat/test-math_dgr-ds.dataFrameSort.R +++ b/tests/testthat/test-math_dgr-ds.dataFrameSort.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('ds.dataFrameSort::expt_dgr::setup') +# context('ds.dataFrameSort::expt_dgr::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSort.R') @@ -21,7 +22,7 @@ source('definition_tests/def-ds.dataFrameSort.R') # Tests # -context("ds.dataFrameSort::math_dgr::closure::multiple") +# context("ds.dataFrameSort::math_dgr::closure::multiple") test_that('server set %in% local set', { connect.all.datasets() @@ -43,7 +44,7 @@ test_that('server set %in% local set', }) -context("ds.dataFrameSort::math_dgr::closure::simple") +# context("ds.dataFrameSort::math_dgr::closure::simple") test_that('server set %in% local set', { connect.dataset.1() diff --git a/tests/testthat/test-math_dgr-ds.dataFrameSubset.R b/tests/testthat/test-math_dgr-ds.dataFrameSubset.R index 39ac712ba..c9a8e176e 100644 --- a/tests/testthat/test-math_dgr-ds.dataFrameSubset.R +++ b/tests/testthat/test-math_dgr-ds.dataFrameSubset.R @@ -1,3 +1,10 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# # You should have received a copy of the GNU General Public License # along with this program. If not, see . #------------------------------------------------------------------------------- @@ -6,7 +13,7 @@ # Set up # -context('ds.dataFrameSubset::expt_dgr::setup') +# context('ds.dataFrameSubset::expt_dgr::setup') source('connection_to_datasets/init_testing_datasets.R') source('definition_tests/def-ds.dataFrameSubset.R') @@ -15,7 +22,7 @@ source('definition_tests/def-ds.dataFrameSubset.R') # Tests # -context("ds.dataFrameSubset::math_dgr::closure::multiple") +# context("ds.dataFrameSubset::math_dgr::closure::multiple") test_that('server set %in% local set', { connect.all.datasets() @@ -33,7 +40,7 @@ test_that('server set %in% local set', # .closure.test("D","POSITIVE_NUMERIC","NON_NEGATIVE_NUMERIC","<=",FALSE,"subset.server",local.df.list) }) -context("ds.dataFrameSubset::math_dgr::closure::simple") +# context("ds.dataFrameSubset::math_dgr::closure::simple") test_that('server set %in% local set', { connect.dataset.2() diff --git a/tests/testthat/test-math_dgr-ds.skewness.R b/tests/testthat/test-math_dgr-ds.skewness.R index d6c8ab219..d743de0b1 100644 --- a/tests/testthat/test-math_dgr-ds.skewness.R +++ b/tests/testthat/test-math_dgr-ds.skewness.R @@ -1,7 +1,18 @@ +#------------------------------------------------------------------------------- +# Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# +# This program and the accompanying materials +# are made available under the terms of the GNU Public License v3.0. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +#------------------------------------------------------------------------------- + source("connection_to_datasets/init_testing_datasets.R") source("definition_tests/def-ds.skewness.R") -context("ds.skewness::math_dgr::mean.median.mode::multiple") +# context("ds.skewness::math_dgr::mean.median.mode::multiple") test_that("skewness >0 & mode0 & mode0 & Q3-Q2>Q2-Q1 or skewness<0 & Q3-Q2 appears valid in all sources") }) -context("ds.dataFrameSubset::smk::create a subset dataframe, based on scalar") +# context("ds.dataFrameSubset::smk::create a subset dataframe, based on scalar") test_that("dataFrameSubset_exists scalar", { myvectors <- c('D$LAB_TSC', 'D$LAB_HDL', 'D$PM_BMI_CATEGORICAL') ds.dataFrame(x=myvectors, newobj="unsubset_df") @@ -100,7 +101,7 @@ test_that("dataFrameSubset_exists scalar", { # Done # -context("ds.dataFrameSubset::smk::shutdown") +# context("ds.dataFrameSubset::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "unsubset_df", "subset_df")) @@ -108,4 +109,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dataFrameSubset::smk::down") +# context("ds.dataFrameSubset::smk::down") diff --git a/tests/testthat/test-smk-ds.dim.R b/tests/testthat/test-smk-ds.dim.R index c1d1d9b5a..3c8caf0e1 100644 --- a/tests/testthat/test-smk-ds.dim.R +++ b/tests/testthat/test-smk-ds.dim.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("ds.dim::smk::setup") +# context("ds.dim::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.dim::smk") +# context("ds.dim::smk") test_that("simple dim, both", { dim.res <- ds.dim('D', type='both') @@ -43,7 +44,7 @@ test_that("simple dim, both", { expect_equal(dim.res$`dimensions of D in combined studies`[[2]], 1) }) -context("ds.dim::smk") +# context("ds.dim::smk") test_that("simple dim, split", { dim.res <- ds.dim('D', type='split') @@ -59,7 +60,7 @@ test_that("simple dim, split", { expect_equal(dim.res$`dimensions of D in sim3`[[2]], 1) }) -context("ds.dim::smk") +# context("ds.dim::smk") test_that("simple dim, combine", { dim.res <- ds.dim('D', type='combine') @@ -73,7 +74,7 @@ test_that("simple dim, combine", { # Done # -context("ds.dim::smk::shutdown") +# context("ds.dim::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -81,4 +82,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.dim::smk::done") +# context("ds.dim::smk::done") diff --git a/tests/testthat/test-smk-ds.dmtC2S.R b/tests/testthat/test-smk-ds.dmtC2S.R index fb56fb435..5a1ba2737 100644 --- a/tests/testthat/test-smk-ds.dmtC2S.R +++ b/tests/testthat/test-smk-ds.dmtC2S.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.dmtC2S::smk::setup") +# context("ds.dmtC2S::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -25,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.dmtC2S::smk::data.frame") +# context("ds.dmtC2S::smk::data.frame") test_that("simple dmtC2S - data.frame", { a <- data.frame(c(1, 2, 3, 4)) b <- data.frame(c(2, 3, 4, 1)) @@ -44,7 +44,7 @@ test_that("simple dmtC2S - data.frame", { expect_true(all(c("data.frame") %in% res.class$sim3)) }) -context("ds.dmtC2S::smk::matrix") +# context("ds.dmtC2S::smk::matrix") test_that("simple dmtC2S - matrix", { a <- c(1, 2, 3, 4, 2, 3, 4, 1, 3) cm <- matrix(a, nrow = 3, ncol = 3, byrow = TRUE) @@ -61,7 +61,7 @@ test_that("simple dmtC2S - matrix", { expect_true(all(c("matrix", "array") %in% res.class$sim3)) }) -context("ds.dmtC2S::smk::tibble") +# context("ds.dmtC2S::smk::tibble") test_that("simple dmtC2S - tibble", { a <- data.frame(c(1, 2, 3, 4)) b <- data.frame(c(2, 3, 4, 1)) @@ -84,7 +84,7 @@ test_that("simple dmtC2S - tibble", { # Done # -context("ds.dmtC2S::smk::shutdown") +# context("ds.dmtC2S::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "dataframe.newobj", "matrix.newobj", "tibble.newobj")) @@ -92,4 +92,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.dmtC2S::smk::done") +# context("ds.dmtC2S::smk::done") diff --git a/tests/testthat/test-smk-ds.elspline.R b/tests/testthat/test-smk-ds.elspline.R index 72753d624..aa8d3d787 100644 --- a/tests/testthat/test-smk-ds.elspline.R +++ b/tests/testthat/test-smk-ds.elspline.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("ds.elspline::smk::setup") +# context("ds.elspline::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.elspline::smk::test1") +# context("ds.elspline::smk::test1") test_that("elspline", { ds.elspline(x="D$PM_BMI_CONTINUOUS", n=3, newobj="elsplineDS", datasources=ds.test_env$connections) @@ -74,7 +75,7 @@ test_that("elspline", { }) -context("ds.elspline::smk::test2") +# context("ds.elspline::smk::test2") test_that("elspline", { ds.elspline(x="D$PM_BMI_CONTINUOUS", n=5, newobj="elsplineDS2", datasources=ds.test_env$connections) @@ -132,7 +133,7 @@ test_that("elspline", { # Done # -context("ds.elspline::smk::shutdown") +# context("ds.elspline::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "elsplineDS", "elsplineDS2", "LAB_TRIG")) @@ -140,4 +141,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.elspline::smk::done") +# context("ds.elspline::smk::done") diff --git a/tests/testthat/test-smk-ds.exists.R b/tests/testthat/test-smk-ds.exists.R index 4590bbe44..5f95ea242 100644 --- a/tests/testthat/test-smk-ds.exists.R +++ b/tests/testthat/test-smk-ds.exists.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("ds.exists::smk::setup") +# context("ds.exists::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.exists::smk") +# context("ds.exists::smk") test_that("simple exists", { res <- ds.exists("no_exists_obj") @@ -39,7 +40,7 @@ test_that("simple exists", { # ds.exists(...) can't be used to check within environment -context("ds.exists::smk") +# context("ds.exists::smk") test_that("simple exists, with dollar", { res <- ds.exists('D$LAB_TSC') @@ -52,7 +53,7 @@ test_that("simple exists, with dollar", { expect_equal(res$sim3, FALSE) }) -context("ds.exists::smk") +# context("ds.exists::smk") test_that("simple exists", { ds.assign('D$LAB_TSC', 'exists_obj') @@ -71,7 +72,7 @@ test_that("simple exists", { # Done # -context("ds.exists::smk::shutdown") +# context("ds.exists::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "exists_obj")) @@ -79,4 +80,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.exists::smk::done") +# context("ds.exists::smk::done") diff --git a/tests/testthat/test-smk-ds.exp.R b/tests/testthat/test-smk-ds.exp.R index af09ede61..fa850fb81 100644 --- a/tests/testthat/test-smk-ds.exp.R +++ b/tests/testthat/test-smk-ds.exp.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.exp::smk::setup") +# context("ds.exp::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.exp::smk") +# context("ds.exp::smk") test_that("simple exp", { res1 <- ds.exp("D$LAB_TSC", newobj="exp1_obj") @@ -81,7 +82,7 @@ test_that("simple exp", { # Done # -context("ds.exp::smk::shutdown") +# context("ds.exp::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "exp1_obj", "new_data", "exp2_obj")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.exp::smk::done") +# context("ds.exp::smk::done") diff --git a/tests/testthat/test-smk-ds.gamlss.R b/tests/testthat/test-smk-ds.gamlss.R index c9c084e44..1e4ad232c 100644 --- a/tests/testthat/test-smk-ds.gamlss.R +++ b/tests/testthat/test-smk-ds.gamlss.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("ds.gamlss::smk::setup") +# context("ds.gamlss::smk::setup") connect.studies.dataset.gamlss(list("e3_bw", "e3_gac_None", "hs_zbmi_who", "hs_child_age_None", "h_mbmi_None", "hs_correct_raven", "hs_wgtgain_None")) @@ -25,7 +26,7 @@ test_that("setup", { # Tests # -context("ds.gamlss::smk::mod1") +# context("ds.gamlss::smk::mod1") test_that("gamlss, birth weight", { model_e3_bw.DS <- ds.gamlss(formula = 'e3_bw ~ e3_gac_None', sigma.formula = 'e3_bw ~ e3_gac_None', @@ -111,7 +112,7 @@ test_that("gamlss, birth weight", { expect_equal(as.numeric(model_e3_bw.DS$study1$centiles[9,'per']), 99.3410214, tolerance=1e-7) }) -context("ds.gamlss::smk::mod2") +# context("ds.gamlss::smk::mod2") test_that("gamlss, Z BMI", { model_zbmi_who.DS <- ds.gamlss(formula = 'hs_zbmi_who ~ hs_child_age_None+h_mbmi_None', sigma.formula = 'hs_zbmi_who ~ hs_child_age_None', @@ -199,7 +200,7 @@ test_that("gamlss, Z BMI", { }) -context("ds.gamlss::smk::mod3") +# context("ds.gamlss::smk::mod3") test_that("gamlss, RAVEN TEST", { ds.dataFrameSort(df.name = 'D', sort.key.name = 'D$hs_correct_raven', newobj = 'D2') @@ -291,7 +292,7 @@ test_that("gamlss, RAVEN TEST", { expect_equal(as.numeric(model_correct_raven.DS$study1$centiles[9,'per']), 100.000000, tolerance=1e-7) }) -context("ds.gamlss::smk::mod4") +# context("ds.gamlss::smk::mod4") test_that("gamlss, WEIGHT GAIN", { model_wgtgain.DS <- ds.gamlss(formula = 'hs_wgtgain_None ~ (e3_bw)', sigma.formula = 'hs_wgtgain_None ~ (e3_bw)', @@ -381,7 +382,7 @@ test_that("gamlss, WEIGHT GAIN", { # Done # -context("ds.gamlss::smk::shutdown") +# context("ds.gamlss::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D2", "z_scores_e3_bw", "z_scores_hs_correct_raven", "z_scores_hs_wgtgain_None", @@ -390,4 +391,4 @@ test_that("shutdown", { disconnect.studies.dataset.gamlss() -context("ds.gamlss::smk::done") +# context("ds.gamlss::smk::done") diff --git a/tests/testthat/test-smk-ds.getWGSR.R b/tests/testthat/test-smk-ds.getWGSR.R index b11e59993..c5034a717 100644 --- a/tests/testthat/test-smk-ds.getWGSR.R +++ b/tests/testthat/test-smk-ds.getWGSR.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.getWGSR::smk::setup") +# context("ds.getWGSR::smk::setup") connect.studies.dataset.anthro(list("age", "sex", "weight", "height", "muac")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.getWGSR::smk") +# context("ds.getWGSR::smk") test_that("simple getWGSR", { res <- ds.getWGSR('D$sex', 'D$weight', 'D$height', 'wfh', newobj='newobj.getwgsr') @@ -61,7 +62,7 @@ test_that("simple getWGSR", { # Done # -context("ds.getWGSR::smk::shutdown") +# context("ds.getWGSR::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "newobj.getwgsr")) @@ -69,4 +70,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.getWGSR::smk::done") +# context("ds.getWGSR::smk::done") diff --git a/tests/testthat/test-smk-ds.glm-binomial.R b/tests/testthat/test-smk-ds.glm-binomial.R index 133a93e18..666188efd 100644 --- a/tests/testthat/test-smk-ds.glm-binomial.R +++ b/tests/testthat/test-smk-ds.glm-binomial.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.glm::smk::binomial::setup") +# context("ds.glm::smk::binomial::setup") connect.studies.dataset.cnsim(list("DIS_DIAB", "GENDER", "PM_BMI_CONTINUOUS", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glm::smk::binomial") +# context("ds.glm::smk::binomial") test_that("glm_binomial", { res <- ds.glm('D$DIS_DIAB~D$GENDER*D$PM_BMI_CONTINUOUS+D$LAB_HDL', family="binomial", checks=FALSE) @@ -50,7 +51,7 @@ test_that("glm_binomial", { expect_equal(res$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) -context("ds.glm::smk::binomial, with check") +# context("ds.glm::smk::binomial, with check") test_that("glm_binomial, with check", { expect_warning(res <- ds.glm('D$DIS_DIAB~D$GENDER*D$PM_BMI_CONTINUOUS+D$LAB_HDL', family="binomial", checks=TRUE), "NAs introduced by coercion") @@ -80,7 +81,7 @@ test_that("glm_binomial, with check", { # Done # -context("ds.glm::smk::binomial::shutdown") +# context("ds.glm::smk::binomial::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "DIS_DIAB", "GENDER", "LAB_HDL", "PM_BMI_CONTINUOUS")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.glm::smk::binomial::done") +# context("ds.glm::smk::binomial::done") diff --git a/tests/testthat/test-smk-ds.glm-gaussian.R b/tests/testthat/test-smk-ds.glm-gaussian.R index f482d54b7..569fbdd91 100644 --- a/tests/testthat/test-smk-ds.glm-gaussian.R +++ b/tests/testthat/test-smk-ds.glm-gaussian.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glm::smk::gaussian::setup") +# context("ds.glm::smk::gaussian::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glm::smk::gaussian") +# context("ds.glm::smk::gaussian") test_that("glm_gaussian", { res <- ds.glm('D$LAB_TSC~D$LAB_TRIG',family="gaussian",checks=FALSE) @@ -50,7 +51,7 @@ test_that("glm_gaussian", { expect_equal(res$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) -context("ds.glm::smk::gaussian, with check") +# context("ds.glm::smk::gaussian, with check") test_that("glm_gaussian, with check", { expect_warning(res <- ds.glm('D$LAB_TSC~D$LAB_TRIG', family="gaussian", checks=TRUE), "NAs introduced by coercion") @@ -80,7 +81,7 @@ test_that("glm_gaussian, with check", { # Done # -context("ds.glm::smk::gaussian::shutdown") +# context("ds.glm::smk::gaussian::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "LAB_TSC")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.glm::smk::gaussian::done") +# context("ds.glm::smk::gaussian::done") diff --git a/tests/testthat/test-smk-ds.glm-poisson.R b/tests/testthat/test-smk-ds.glm-poisson.R index a8385bfb4..19c56ebc7 100644 --- a/tests/testthat/test-smk-ds.glm-poisson.R +++ b/tests/testthat/test-smk-ds.glm-poisson.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.glm::smk::poisson::setup") +# context("ds.glm::smk::poisson::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glm::smk::poisson") +# context("ds.glm::smk::poisson") test_that("glm_gaussian", { res <- ds.glm("D$survtime~1+D$time.id+D$female", family="poisson", checks=FALSE) @@ -50,7 +51,7 @@ test_that("glm_gaussian", { expect_equal(res$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) -context("ds.glm::smk::poisson, with check") +# context("ds.glm::smk::poisson, with check") test_that("glm_gaussian, which check", { expect_warning(res <- ds.glm("D$survtime~1+D$time.id+D$female", family="poisson", checks=TRUE), "NAs introduced by coercion") @@ -80,7 +81,7 @@ test_that("glm_gaussian, which check", { # Done # -context("ds.glm::smk::poisson::shutdown") +# context("ds.glm::smk::poisson::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "female", "survtime", "time.id")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.glm::smk::poisson::done") +# context("ds.glm::smk::poisson::done") diff --git a/tests/testthat/test-smk-ds.glmPredict-binomial.R b/tests/testthat/test-smk-ds.glmPredict-binomial.R index 59ec5438d..12570b9c5 100644 --- a/tests/testthat/test-smk-ds.glmPredict-binomial.R +++ b/tests/testthat/test-smk-ds.glmPredict-binomial.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmPredict::smk::binomial::setup") +# context("ds.glmPredict::smk::binomial::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmPredict::smk::binomial::without_newobj") +# context("ds.glmPredict::smk::binomial::without_newobj") test_that("simple glmPredict, binomial, without newobj, se.fit=FALSE",{ glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -106,7 +107,7 @@ test_that("simple glmPredict, binomial, without newobj, se.fit=FALSE",{ }) -context("ds.glmPredict::smk::binomial::with_newobj") +# context("ds.glmPredict::smk::binomial::with_newobj") test_that("simple glmPredict, binomial, with newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -187,7 +188,7 @@ test_that("simple glmPredict, binomial, with newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 0.029020811, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::binomial::sefit_true") +# context("ds.glmPredict::smk::binomial::sefit_true") test_that("simple glmPredict, binomial, with newobj, se.fit=TRUE", { glmSLMA.res <- ds.glmSLMA('D$DIS_DIAB~D$LAB_TRIG', family="binomial", newobj="binomial.glmslma.obj") @@ -318,7 +319,7 @@ test_that("simple glmPredict, binomial, with newobj, se.fit=TRUE", { # Shutdown # -context("ds.glmPredict::smk::binomial::shutdown") +# context("ds.glmPredict::smk::binomial::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "binomial.glmslma.obj", "binomial.glm.predict.obj", "binomial.glm.predict.sefit.obj", "predict_glm" )) @@ -330,4 +331,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmPredict::smk::binomial::done") +# context("ds.glmPredict::smk::binomial::done") diff --git a/tests/testthat/test-smk-ds.glmPredict-gaussian.R b/tests/testthat/test-smk-ds.glmPredict-gaussian.R index e810f118c..934aba3e7 100644 --- a/tests/testthat/test-smk-ds.glmPredict-gaussian.R +++ b/tests/testthat/test-smk-ds.glmPredict-gaussian.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmPredict::smk::gaussian::setup") +# context("ds.glmPredict::smk::gaussian::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.glmPredict::smk::gaussian::without_newobj") +# context("ds.glmPredict::smk::gaussian::without_newobj") test_that("simple glmPredict, gaussian, without newobj, se.fit=FALSE",{ glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -104,7 +105,7 @@ test_that("simple glmPredict, gaussian, without newobj, se.fit=FALSE",{ expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.054574, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::gaussian::with_newobj") +# context("ds.glmPredict::smk::gaussian::with_newobj") test_that("simple glmPredict, gaussian, with newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -185,7 +186,7 @@ test_that("simple glmPredict, gaussian, with newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.054574, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::gaussian::sefit_true") +# context("ds.glmPredict::smk::gaussian::sefit_true") test_that("simple glmPredict, gaussian, with newobj, se.fit=TRUE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -316,7 +317,7 @@ test_that("simple glmPredict, gaussian, with newobj, se.fit=TRUE", { # Shutdown # -context("ds.glmPredict::smk::gaussian::shutdown") +# context("ds.glmPredict::smk::gaussian::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "gaussian.glm.predict.obj", "gaussian.glm.predict.sefit.obj", "gaussian.glmslma.obj", "predict_glm" )) @@ -328,4 +329,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmPredict::smk::gaussian::done") +# context("ds.glmPredict::smk::gaussian::done") diff --git a/tests/testthat/test-smk-ds.glmPredict-poisson.R b/tests/testthat/test-smk-ds.glmPredict-poisson.R index 83a0af2b1..d8f830c14 100644 --- a/tests/testthat/test-smk-ds.glmPredict-poisson.R +++ b/tests/testthat/test-smk-ds.glmPredict-poisson.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmPredict::smk::poisson::setup") +# context("ds.glmPredict::smk::poisson::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmPredict::smk::poisson::without_newobj") +# context("ds.glmPredict::smk::poisson::without_newobj") test_that("simple glmPredict, poisson, without newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -105,7 +106,7 @@ test_that("simple glmPredict, poisson, without newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.056664, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::poisson::with_newobj") +# context("ds.glmPredict::smk::poisson::with_newobj") test_that("simple glmPredict, poisson, with newobj, se.fit=FALSE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -186,7 +187,7 @@ test_that("simple glmPredict, poisson, with newobj, se.fit=FALSE", { expect_equal(res$sim3$safe.list$fit.quantiles[[7]], 6.056664, tolerance = ds.test_env$tolerance) }) -context("ds.glmPredict::smk::poisson::sefit_true") +# context("ds.glmPredict::smk::poisson::sefit_true") test_that("simple glmPredict, poisson, with newobj, se.fit=TRUE", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -316,7 +317,7 @@ test_that("simple glmPredict, poisson, with newobj, se.fit=TRUE", { # Shutdown # -context("ds.glmPredict::smk::poisson::shutdown") +# context("ds.glmPredict::smk::poisson::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "poisson.glm.predict.obj", "poisson.glm.predict.sefit.obj", "poisson.glmslma.obj", "predict_glm" )) @@ -328,4 +329,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmPredict::smk::poisson::done") +# context("ds.glmPredict::smk::poisson::done") diff --git a/tests/testthat/test-smk-ds.glmSLMA.R b/tests/testthat/test-smk-ds.glmSLMA.R index 37532ba44..b0769bfdf 100644 --- a/tests/testthat/test-smk-ds.glmSLMA.R +++ b/tests/testthat/test-smk-ds.glmSLMA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.glmSLMA::smk::setup") +# context("ds.glmSLMA::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "MEDI_LPD", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmSLMA::smk::gaussian") +# context("ds.glmSLMA::smk::gaussian") test_that("simple glmSLMA, gaussian", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian") @@ -77,7 +78,7 @@ test_that("simple glmSLMA, gaussian", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::gaussian-assigned") +# context("ds.glmSLMA::smk::gaussian-assigned") test_that("simple glmSLMA, gaussian-assigned", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="glmSLMA_1.newobj") @@ -130,7 +131,7 @@ test_that("simple glmSLMA, gaussian-assigned", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::binomial") +# context("ds.glmSLMA::smk::binomial") test_that("simple glmSLMA, binomial", { ds.asCharacter('D$MEDI_LPD', 'str.medi.lpd') ds.asNumeric('str.medi.lpd', 'num.medi.lpd') @@ -190,7 +191,7 @@ test_that("simple glmSLMA, binomial", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::binomial-assigned") +# context("ds.glmSLMA::smk::binomial-assigned") test_that("simple glmSLMA, binomial-assigned", { ds.asCharacter('D$MEDI_LPD', 'str.medi.lpd') ds.asNumeric('str.medi.lpd', 'num.medi.lpd') @@ -250,7 +251,7 @@ test_that("simple glmSLMA, binomial-assigned", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::poisson") +# context("ds.glmSLMA::smk::poisson") test_that("simple glmSLMA, poisson", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson") @@ -303,7 +304,7 @@ test_that("simple glmSLMA, poisson", { expect_equal(glmSLMA.res$validity.check, " appears valid in all sources") }) -context("ds.glmSLMA::smk::poisson-assigned") +# context("ds.glmSLMA::smk::poisson-assigned") test_that("simple glmSLMA, poisson-assigned", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="glmSLMA_3.newobj") @@ -360,7 +361,7 @@ test_that("simple glmSLMA, poisson-assigned", { # Done # -context("ds.glmSLMA::smk::shutdown") +# context("ds.glmSLMA::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "new.glm.obj", "glmSLMA_1.newobj", "glmSLMA_2.newobj", "glmSLMA_3.newobj", "num.medi.lpd", "num.dis.diab", "num.gender", "str.medi.lpd", "str.dis.diab", "str.gender")) @@ -369,4 +370,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.glmSLMA::smk::done") +# context("ds.glmSLMA::smk::done") diff --git a/tests/testthat/test-smk-ds.glmSummary.R b/tests/testthat/test-smk-ds.glmSummary.R index 68efb105e..c6a827dfc 100644 --- a/tests/testthat/test-smk-ds.glmSummary.R +++ b/tests/testthat/test-smk-ds.glmSummary.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("ds.glmSummary::smk::setup") +# context("ds.glmSummary::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.glmSummary::smk::gaussian") +# context("ds.glmSummary::smk::gaussian") test_that("simple glmSummary, gaussian, without newobj", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj") @@ -87,7 +88,7 @@ test_that("simple glmSummary, gaussian", { expect_equal(class(res$sim3$glm.summary.obj), 'summary.glm') }) -context("ds.glmSummary::smk::poisson") +# context("ds.glmSummary::smk::poisson") test_that("simple glmSummary, poisson, without newobj", { glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj") @@ -154,7 +155,7 @@ test_that("simple glmSummary, poisson", { # Shutdown # -context("ds.glmSummary::smk::shutdown") +# context("ds.glmSummary::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "gaussian.glmslma.obj", "gaussian.glmsummary.obj", "poisson.glmslma.obj", "poisson.glmsummary.obj", "summary_glm.newobj")) @@ -166,4 +167,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.glmSummary::smk::done") +# context("ds.glmSummary::smk::done") diff --git a/tests/testthat/test-smk-ds.glmerSLMA.R b/tests/testthat/test-smk-ds.glmerSLMA.R index 0d9720063..4ad25a02f 100644 --- a/tests/testthat/test-smk-ds.glmerSLMA.R +++ b/tests/testthat/test-smk-ds.glmerSLMA.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 Phase 1 # -context("ds.glmerSLMA::smk::setup - phase 1") +# context("ds.glmerSLMA::smk::setup - phase 1") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests Phase 1 # -context("ds.glmerSLMA::smk::phase 1") +# context("ds.glmerSLMA::smk::phase 1") test_that("simple glmerSLMA tesing (mis)use of arguments", { res = ds.glmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', family='poisson', dataName = "D", start_theta = c(1)) expect_length(res, 8) @@ -74,7 +75,7 @@ test_that("simple glmerSLMA with assign=TRUE", { # Shutdown phase 1 # -context("ds.glmerSLMA::smk::shutdown - phase 1") +# context("ds.glmerSLMA::smk::shutdown - phase 1") test_that("setup", { #note the offset and weights objects below are artefacts @@ -87,7 +88,7 @@ disconnect.studies.dataset.cluster.int() # Set up phase 2 # -context("ds.glmerSLMA::smk::setup - phase 2") +# context("ds.glmerSLMA::smk::setup - phase 2") connect.studies.dataset.cluster.slo(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -99,7 +100,7 @@ test_that("setup", { # Tests phase 2 # -context("ds.glmerSLMA::smk::test - phase 2") +# context("ds.glmerSLMA::smk::test - phase 2") test_that("check slope formulae - 1", { res = ds.glmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor) + (1|idSurgery) + (0+trtGrp|idSurgery)', family='poisson', dataName = 'D', control_type = 'check.conv.grad', control_value = 0.1) @@ -249,7 +250,7 @@ test_that("check slope formulae - 2", { # Shutdown phase 2 # -context("ds.glmerSLMA::smk::shutdown - phase 2") +# context("ds.glmerSLMA::smk::shutdown - phase 2") test_that("setup", { ds_expect_variables(c("D", "offset", "weights")) @@ -261,4 +262,4 @@ disconnect.studies.dataset.cluster.slo() # Done # -context("ds.glmerSLMA::smk::done") +# context("ds.glmerSLMA::smk::done") diff --git a/tests/testthat/test-smk-ds.hetcor.R b/tests/testthat/test-smk-ds.hetcor.R index 7d029fb30..906c1cdd9 100644 --- a/tests/testthat/test-smk-ds.hetcor.R +++ b/tests/testthat/test-smk-ds.hetcor.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("ds.hetcor::smk::setup") +# context("ds.hetcor::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS", "DIS_CVA", "MEDI_LPD", "DIS_DIAB", "DIS_AMI", "GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.hetcor::smk::test1") +# context("ds.hetcor::smk::test1") test_that("hetcor", { ds.dataFrame(c("D$LAB_TSC", "D$LAB_TRIG", "D$LAB_HDL", "D$LAB_GLUC_ADJUSTED", "D$PM_BMI_CONTINUOUS", "D$DIS_CVA", "D$MEDI_LPD", "D$DIS_DIAB", "D$DIS_AMI", "D$GENDER", "D$PM_BMI_CATEGORICAL"), newobj="df") @@ -177,7 +178,7 @@ test_that("hetcor", { # Done # -context("ds.hetcor::smk::shutdown") +# context("ds.hetcor::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "df")) @@ -185,4 +186,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.hetcor::smk::done") +# context("ds.hetcor::smk::done") diff --git a/tests/testthat/test-smk-ds.isNA.R b/tests/testthat/test-smk-ds.isNA.R index fb7213747..a0419eff8 100644 --- a/tests/testthat/test-smk-ds.isNA.R +++ b/tests/testthat/test-smk-ds.isNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.isNA::smk::setup") +# context("ds.isNA::smk::setup") connect.studies.dataset.cnsim(list("LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.isNA::smk") +# context("ds.isNA::smk") res <- ds.isNA(x='D$LAB_HDL') test_that("isNA", { expect_false(res$sim1) @@ -36,7 +37,7 @@ test_that("isNA", { # Tear down # -context("ds.isNA::smk::shutdown") +# context("ds.isNA::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -44,5 +45,5 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.isNA::smk::done") +# context("ds.isNA::smk::done") diff --git a/tests/testthat/test-smk-ds.isValid.R b/tests/testthat/test-smk-ds.isValid.R index 302412ba5..59b72dcce 100644 --- a/tests/testthat/test-smk-ds.isValid.R +++ b/tests/testthat/test-smk-ds.isValid.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.isValid::smk::setup") +# context("ds.isValid::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.isValid::smk") +# context("ds.isValid::smk") test_that("isValid", { res1 <- ds.isValid(x='D$LAB_TSC') @@ -55,7 +56,7 @@ test_that("isValid", { # Tear down # -context("ds.isValid::smk::shutdown") +# context("ds.isValid::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -63,4 +64,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.isValid::smk::done") +# context("ds.isValid::smk::done") diff --git a/tests/testthat/test-smk-ds.kurtosis.R b/tests/testthat/test-smk-ds.kurtosis.R index 76cedb049..297f87e46 100644 --- a/tests/testthat/test-smk-ds.kurtosis.R +++ b/tests/testthat/test-smk-ds.kurtosis.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.kurtosis::smk::setup") +# context("ds.kurtosis::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS")) @@ -27,7 +27,7 @@ test_that("setup", { # Method 1 -context("ds.kurtosis::smk::method 1::split") +# context("ds.kurtosis::smk::method 1::split") test_that("simple kurtosis, method 1, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='split') @@ -128,7 +128,7 @@ test_that("simple kurtosis, method 1, split, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 1::combine") +# context("ds.kurtosis::smk::method 1::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='combine') @@ -199,7 +199,7 @@ test_that("simple kurtosis, method 1, combine, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 1::both") +# context("ds.kurtosis::smk::method 1::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='both') @@ -342,7 +342,7 @@ test_that("simple kurtosis, method 1, both, on PM_BMI_CONTINUOUS", { # Method 2 -context("ds.kurtosis::smk::method 2::split") +# context("ds.kurtosis::smk::method 2::split") test_that("simple kurtosis, method 2, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='split') @@ -443,7 +443,7 @@ test_that("simple kurtosis, method 2, split, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 2::combine") +# context("ds.kurtosis::smk::method 2::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='combine') @@ -514,7 +514,7 @@ test_that("simple kurtosis, method 2, combine, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 2::both") +# context("ds.kurtosis::smk::method 2::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='both') @@ -657,7 +657,7 @@ test_that("simple kurtosis, method 2, both, on PM_BMI_CONTINUOUS", { # Method 3 -context("ds.kurtosis::smk::method 3::split") +# context("ds.kurtosis::smk::method 3::split") test_that("simple kurtosis, method 3, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='split') @@ -758,7 +758,7 @@ test_that("simple kurtosis, method 3, split, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 3::combine") +# context("ds.kurtosis::smk::method 3::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='combine') @@ -829,7 +829,7 @@ test_that("simple kurtosis, method 3, combine, on PM_BMI_CONTINUOUS", { expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.kurtosis::smk::method 3::both") +# context("ds.kurtosis::smk::method 3::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='both') @@ -974,7 +974,7 @@ test_that("simple kurtosis, method 3, both, on PM_BMI_CONTINUOUS", { # Done # -context("ds.kurtosis::smk::shutdown") +# context("ds.kurtosis::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -982,4 +982,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.kurtosis::smk::done") +# context("ds.kurtosis::smk::done") diff --git a/tests/testthat/test-smk-ds.length.R b/tests/testthat/test-smk-ds.length.R index 58d85b33e..b7c9bd764 100644 --- a/tests/testthat/test-smk-ds.length.R +++ b/tests/testthat/test-smk-ds.length.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.length::smk::setup") +# context("ds.length::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.length::smk") +# context("ds.length::smk") test_that("basic length, both", { res.length <- ds.length('D$LAB_TSC', type='both') @@ -81,7 +82,7 @@ test_that("basic length, combine", { # Done # -context("ds.length::smk::shutdown") +# context("ds.length::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.length::smk::done") +# context("ds.length::smk::done") diff --git a/tests/testthat/test-smk-ds.levels.R b/tests/testthat/test-smk-ds.levels.R index cc262a1ed..022758937 100644 --- a/tests/testthat/test-smk-ds.levels.R +++ b/tests/testthat/test-smk-ds.levels.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("ds.levels::smk::setup") +# context("ds.levels::smk::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.levels::smk") +# context("ds.levels::smk") test_that("simple levels", { ds.asFactor("D$GENDER", newobj.name = "gender") @@ -51,7 +52,7 @@ test_that("simple levels", { expect_equal(res$sim3$Levels[2], "1") }) -context("ds.levels::smk") +# context("ds.levels::smk") test_that("simple levels", { ds.asFactor("D$PM_BMI_CATEGORICAL", newobj.name = "pm_bmi_categorical") @@ -85,7 +86,7 @@ test_that("simple levels", { # Done # -context("ds.levels::smk::shutdown") +# context("ds.levels::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "gender", "pm_bmi_categorical")) @@ -93,5 +94,5 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.levels::smk::done") +# context("ds.levels::smk::done") diff --git a/tests/testthat/test-smk-ds.lexis.R b/tests/testthat/test-smk-ds.lexis.R index 2ad3b717d..c0c302339 100644 --- a/tests/testthat/test-smk-ds.lexis.R +++ b/tests/testthat/test-smk-ds.lexis.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.lexis::smk::setup") +# context("ds.lexis::smk::setup") connect.studies.dataset.survival(list("id", "starttime", "endtime", "cens", "age.60")) @@ -25,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lexis::smk") +# context("ds.lexis::smk") test_that("simple lexis", { res <- ds.lexis(data='D', intervalWidth = c(1.0, 1.5, 2.5), idCol = 'D$id', entryCol = 'D$starttime', exitCol = 'D$endtime', statusCol = 'D$cens', variables = c('D$age.60'), expandDF = 'EM.new') @@ -55,7 +55,7 @@ test_that("simple lexis", { # Done # -context("ds.lexis::smk::shutdown") +# context("ds.lexis::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "EM.new", "messageobj")) @@ -63,4 +63,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.lexis::smk::done") +# context("ds.lexis::smk::done") diff --git a/tests/testthat/test-smk-ds.list.R b/tests/testthat/test-smk-ds.list.R index d369bedfc..85ff10d86 100644 --- a/tests/testthat/test-smk-ds.list.R +++ b/tests/testthat/test-smk-ds.list.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.list::smk::setup") +# context("ds.list::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.list::smk") +# context("ds.list::smk") test_that("Is List", { myobjects <- c('D$LAB_TSC', 'D$LAB_HDL') res <- ds.list(x=myobjects, newobj='my_newobj') @@ -72,7 +73,7 @@ test_that("Is List", { # Tear down # -context("ds.list::smk::shutdown") +# context("ds.list::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "my_newobj")) @@ -80,4 +81,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.list::smk::down") +# context("ds.list::smk::down") diff --git a/tests/testthat/test-smk-ds.listClientsideFunctions.R b/tests/testthat/test-smk-ds.listClientsideFunctions.R index 31b053eb1..befb73246 100644 --- a/tests/testthat/test-smk-ds.listClientsideFunctions.R +++ b/tests/testthat/test-smk-ds.listClientsideFunctions.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.listClientsideFunctions::smk::setup") +# context("ds.listClientsideFunctions::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -25,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.listClientsideFunctions::smk::check results") +# context("ds.listClientsideFunctions::smk::check results") test_that("check results", { output <- list( "ds.abs", @@ -152,7 +152,7 @@ test_that("check results", { # Done # -context("ds.listClientsideFunctions::smk::shutdown") +# context("ds.listClientsideFunctions::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -160,4 +160,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.listClientsideFunctions::smk::done") +# context("ds.listClientsideFunctions::smk::done") diff --git a/tests/testthat/test-smk-ds.listDisclosureSettings.R b/tests/testthat/test-smk-ds.listDisclosureSettings.R index e1b136951..2d8e34842 100644 --- a/tests/testthat/test-smk-ds.listDisclosureSettings.R +++ b/tests/testthat/test-smk-ds.listDisclosureSettings.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.listDisclosureSettings::smk::setup") +# context("ds.listDisclosureSettings::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.listDisclosureSettings::smk::check results") +# context("ds.listDisclosureSettings::smk::check results") test_that("check results", { res <- ds.listDisclosureSettings() @@ -78,7 +79,7 @@ test_that("check results", { # Done # -context("ds.listDisclosureSettings::smk::shutdown") +# context("ds.listDisclosureSettings::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -86,4 +87,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.listDisclosureSettings::smk::down") +# context("ds.listDisclosureSettings::smk::down") diff --git a/tests/testthat/test-smk-ds.listServersideFunctions.R b/tests/testthat/test-smk-ds.listServersideFunctions.R index 4e098b128..0e3221fb2 100644 --- a/tests/testthat/test-smk-ds.listServersideFunctions.R +++ b/tests/testthat/test-smk-ds.listServersideFunctions.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -19,7 +19,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) # Tests # -context("ds.listServersideFunctions::smk::check results") +# context("ds.listServersideFunctions::smk::check results") test_that("check results", { assign.functions <- factor(c( "BooleDS", "abs", "absDS", "acos", "as.character", "as.null", "as.numeric", "asCharacterDS", "asDataMatrixDS", diff --git a/tests/testthat/test-smk-ds.lmerSLMA.R b/tests/testthat/test-smk-ds.lmerSLMA.R index c552a65ff..7d352a9c2 100644 --- a/tests/testthat/test-smk-ds.lmerSLMA.R +++ b/tests/testthat/test-smk-ds.lmerSLMA.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 phase 1 # -context("ds.lmerSLMA::smk::setup phase 1") +# context("ds.lmerSLMA::smk::setup phase 1") connect.studies.dataset.cluster.int(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::smk::phase 1") +# context("ds.lmerSLMA::smk::phase 1") test_that("simple lmerSLMA", { res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = "D") @@ -75,7 +76,7 @@ test_that("test offsets and weights", { # Shutdown # -context("ds.lmerSLMA::smk::shutdown phase 1") +# context("ds.lmerSLMA::smk::shutdown phase 1") test_that("shutdown", { #note the offset and weights objects below are artefacts @@ -89,7 +90,7 @@ disconnect.studies.dataset.cluster.int() # Set up # -context("ds.lmerSLMA::smk::setup phase 2") +# context("ds.lmerSLMA::smk::setup phase 2") connect.studies.dataset.cluster.slo(list("incid_rate", "trtGrp", "Male", "idDoctor", "BMI", "idSurgery")) @@ -101,7 +102,7 @@ test_that("setup", { # Tests # -context("ds.lmerSLMA::smk::test phase 2") +# context("ds.lmerSLMA::smk::test phase 2") test_that("check slope formulae", { res = ds.lmerSLMA(formula = 'BMI ~ trtGrp + Male + (1|idDoctor) + (1|idSurgery) + (0+trtGrp|idSurgery)', dataName = 'D', control_type = 'check.conv.grad',control_value = 0.1) @@ -251,7 +252,7 @@ test_that("check slope formulae", { # Shutdown # -context("ds.lmerSLMA::smk::shutdown phase 2") +# context("ds.lmerSLMA::smk::shutdown phase 2") test_that("shutdown", { ds_expect_variables(c("D", "offset", "weights")) @@ -263,4 +264,4 @@ disconnect.studies.dataset.cluster.slo() # Done # -context("ds.lmerSLMA::smk::done") +# context("ds.lmerSLMA::smk::done") diff --git a/tests/testthat/test-smk-ds.log.R b/tests/testthat/test-smk-ds.log.R index cd18e6f1f..c857408db 100644 --- a/tests/testthat/test-smk-ds.log.R +++ b/tests/testthat/test-smk-ds.log.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("ds.log::smk::setup") +# context("ds.log::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.log::smk") +# context("ds.log::smk") test_that("simple log", { res1 <- ds.log("D$LAB_TSC", newobj="log1_obj") @@ -81,7 +82,7 @@ test_that("simple log", { # Done # -context("ds.log::smk::shutdown") +# context("ds.log::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "new_data", "log1_obj", "log2_obj")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.log::smk::done") +# context("ds.log::smk::done") diff --git a/tests/testthat/test-smk-ds.look.R b/tests/testthat/test-smk-ds.look.R index c8167430c..f4a656837 100644 --- a/tests/testthat/test-smk-ds.look.R +++ b/tests/testthat/test-smk-ds.look.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("ds.look::smk::setup") +# context("ds.look::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.look::smk") +# context("ds.look::smk") test_that("simple look", { res <- ds.look("lengthDS('D$LAB_TSC')") @@ -39,7 +40,7 @@ test_that("simple look", { # Done # -context("ds.look::smk::shutdown") +# context("ds.look::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -47,4 +48,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.look::smk::done") +# context("ds.look::smk::done") diff --git a/tests/testthat/test-smk-ds.ls.R b/tests/testthat/test-smk-ds.ls.R index 1a9afe3d4..91dd745a4 100644 --- a/tests/testthat/test-smk-ds.ls.R +++ b/tests/testthat/test-smk-ds.ls.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("ds.ls::smk::setup") +# context("ds.ls::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ls::smk") +# context("ds.ls::smk") test_that("simple ls", { res <- ds.ls() @@ -107,7 +108,7 @@ test_that("simple ls, with envir, with wildcard prefix", { # Shutdown # -context("ds.ls::smk::shutdown") +# context("ds.ls::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -119,4 +120,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.ls::smk::done") +# context("ds.ls::smk::done") diff --git a/tests/testthat/test-smk-ds.lspline.R b/tests/testthat/test-smk-ds.lspline.R index 9529babd7..08d45470d 100644 --- a/tests/testthat/test-smk-ds.lspline.R +++ b/tests/testthat/test-smk-ds.lspline.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("ds.lspline::smk::setup") +# context("ds.lspline::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.lspline::smk::test1") +# context("ds.lspline::smk::test1") test_that("lspline", { ds.lspline(x="D$PM_BMI_CONTINUOUS", knots=c(15,25,35), newobj="lsplineDS", datasources=ds.test_env$connections) @@ -81,7 +82,7 @@ test_that("lspline", { # Done # -context("ds.lspline::smk::shutdown") +# context("ds.lspline::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "lsplineDS")) @@ -89,4 +90,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.qlspline::smk::done") +# context("ds.qlspline::smk::done") diff --git a/tests/testthat/test-smk-ds.make.R b/tests/testthat/test-smk-ds.make.R index 57565fbe5..cadb04707 100644 --- a/tests/testthat/test-smk-ds.make.R +++ b/tests/testthat/test-smk-ds.make.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.make::smk::setup") +# context("ds.make::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.make::smk") +# context("ds.make::smk") test_that("simple make", { res <- ds.make("(D$LAB_TSC*D$LAB_TRIG*D$LAB_HDL)", "maded.rand") @@ -33,7 +34,7 @@ test_that("simple make", { expect_equal(res$validity.check, " appears valid in all sources") }) -context("ds.make::smk") +# context("ds.make::smk") test_that("simple make", { res <- ds.make("(D$LAB_TSC*10)", "maded.rand") @@ -42,7 +43,7 @@ test_that("simple make", { expect_equal(res$validity.check, " appears valid in all sources") }) -context("ds.make::smk") +# context("ds.make::smk") test_that("simple make", { res <- ds.make("(D$LAB_TSC)*10", "maded.rand") @@ -55,7 +56,7 @@ test_that("simple make", { # Done # -context("ds.make::smk::shutdown") +# context("ds.make::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "maded.rand")) @@ -63,4 +64,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.make::smk::done") +# context("ds.make::smk::done") diff --git a/tests/testthat/test-smk-ds.matrix.R b/tests/testthat/test-smk-ds.matrix.R index c9295bd9a..d48367603 100644 --- a/tests/testthat/test-smk-ds.matrix.R +++ b/tests/testthat/test-smk-ds.matrix.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("ds.matrix::smk::setup") +# context("ds.matrix::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrix::smk") +# context("ds.matrix::smk") test_that("simplest ds.matrix", { matrix <- c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11) @@ -46,7 +47,7 @@ test_that("simplest ds.matrix", { # Tear down # -context("ds.matrix::smk::shutdown") +# context("ds.matrix::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj")) @@ -54,4 +55,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrix::smk::done") +# context("ds.matrix::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDet.R b/tests/testthat/test-smk-ds.matrixDet.R index 3cf8f8b50..74626cbc4 100644 --- a/tests/testthat/test-smk-ds.matrixDet.R +++ b/tests/testthat/test-smk-ds.matrixDet.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("ds.matrixDet::smk::setup") +# context("ds.matrixDet::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDet::smk") +# context("ds.matrixDet::smk") test_that("simplest ds.matrixDet", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -47,7 +48,7 @@ test_that("simplest ds.matrixDet", { # Tear down # -context("ds.matrixDet::smk::shutdown") +# context("ds.matrixDet::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixdet.newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDet::smk::done") +# context("ds.matrixDet::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDet.report.R b/tests/testthat/test-smk-ds.matrixDet.report.R index 5854fbde3..20850a5a3 100644 --- a/tests/testthat/test-smk-ds.matrixDet.report.R +++ b/tests/testthat/test-smk-ds.matrixDet.report.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("ds.matrixDet.report::smk::setup") +# context("ds.matrixDet.report::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDet.report::smk") +# context("ds.matrixDet.report::smk") test_that("simplest ds.matrixDet.report", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -51,7 +52,7 @@ test_that("simplest ds.matrixDet.report", { # Tear down # -context("ds.matrixDet.report::smk::shutdown") +# context("ds.matrixDet.report::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj")) @@ -59,4 +60,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDet.report::smk::done") +# context("ds.matrixDet.report::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDiag.R b/tests/testthat/test-smk-ds.matrixDiag.R index 14bc8baba..2a9b30d75 100644 --- a/tests/testthat/test-smk-ds.matrixDiag.R +++ b/tests/testthat/test-smk-ds.matrixDiag.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("ds.matrixDiag::smk::setup") +# context("ds.matrixDiag::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDiag::smk") +# context("ds.matrixDiag::smk") test_that("simplest ds.matrixDiag", { matrix <- c(0, 1, 2, 3, 4, 5) @@ -42,7 +43,7 @@ test_that("simplest ds.matrixDiag", { expect_true("matrix" %in% check.class$sim3) }) -context("ds.matrixDiag::smk") +# context("ds.matrixDiag::smk") test_that("simplest ds.matrixDiag", { matrix <- c(0, 1, 2, 3, 4, 5) @@ -64,7 +65,7 @@ test_that("simplest ds.matrixDiag", { # Tear down # -context("ds.matrixDiag::smk::shutdown") +# context("ds.matrixDiag::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix_diag", "matrixdiag.newobj")) @@ -72,4 +73,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDiag::smk::done") +# context("ds.matrixDiag::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixDimnames.R b/tests/testthat/test-smk-ds.matrixDimnames.R index f39a04799..6ac87d2ff 100644 --- a/tests/testthat/test-smk-ds.matrixDimnames.R +++ b/tests/testthat/test-smk-ds.matrixDimnames.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("ds.matrixDimnames::smk::setup") +# context("ds.matrixDimnames::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixDimnames::smk") +# context("ds.matrixDimnames::smk") test_that("simplest ds.matrixDimnames", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -50,7 +51,7 @@ test_that("simplest ds.matrixDimnames", { # Tear down # -context("ds.matrixDimnames::smk::shutdown") +# context("ds.matrixDimnames::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixdimnames.newobj")) @@ -58,4 +59,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixDimnames::smk::done") +# context("ds.matrixDimnames::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixInvert.R b/tests/testthat/test-smk-ds.matrixInvert.R index b0ab7f41e..8cd89a415 100644 --- a/tests/testthat/test-smk-ds.matrixInvert.R +++ b/tests/testthat/test-smk-ds.matrixInvert.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("ds.matrixInvert::smk::setup") +# context("ds.matrixInvert::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixInvert::smk") +# context("ds.matrixInvert::smk") test_that("simplest ds.matrixInvert", { matrix <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) @@ -47,7 +48,7 @@ test_that("simplest ds.matrixInvert", { # Tear down # -context("ds.matrixInvert::smk::shutdown") +# context("ds.matrixInvert::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixinvert.newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixInvert::smk::done") +# context("ds.matrixInvert::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixMult.R b/tests/testthat/test-smk-ds.matrixMult.R index 76ddb9af3..001e36efb 100644 --- a/tests/testthat/test-smk-ds.matrixMult.R +++ b/tests/testthat/test-smk-ds.matrixMult.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("ds.matrixMult::smk::setup") +# context("ds.matrixMult::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixMult::smk") +# context("ds.matrixMult::smk") test_that("simplest ds.matrixMult", { matrix1 <- c(-2, 1, 3, 0, -1, 1, 1, 2, 0) matrix2 <- c(-2, 1, 3, 1, -1, 1, 1, 2, 1) @@ -49,7 +50,7 @@ test_that("simplest ds.matrixMult", { # Tear down # -context("ds.matrixMult::smk::shutdown") +# context("ds.matrixMult::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "mat1", "mat2", "matrixmult.newobj")) @@ -57,4 +58,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixMult::smk::done") +# context("ds.matrixMult::smk::done") diff --git a/tests/testthat/test-smk-ds.matrixTranspose.R b/tests/testthat/test-smk-ds.matrixTranspose.R index 234fbb383..fa1920a78 100644 --- a/tests/testthat/test-smk-ds.matrixTranspose.R +++ b/tests/testthat/test-smk-ds.matrixTranspose.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("ds.matrixTranspose::smk::setup") +# context("ds.matrixTranspose::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.matrixTranspose::smk") +# context("ds.matrixTranspose::smk") test_that("simplest ds.matrixTranspose", { matrix <- c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11) @@ -47,7 +48,7 @@ test_that("simplest ds.matrixTranspose", { # Tear down # -context("ds.matrixTranspose::smk::shutdown") +# context("ds.matrixTranspose::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "matrix.newobj", "matrixtranspose.newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.matrixTranspose::smk::done") +# context("ds.matrixTranspose::smk::done") diff --git a/tests/testthat/test-smk-ds.mean.R b/tests/testthat/test-smk-ds.mean.R index be89553c5..5b2d7360e 100644 --- a/tests/testthat/test-smk-ds.mean.R +++ b/tests/testthat/test-smk-ds.mean.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.mean::smk::setup") +# context("ds.mean::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.mean::smk::type=combine") +# context("ds.mean::smk::type=combine") test_that("mean values [combine]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -60,7 +61,7 @@ test_that("mean values [combine]", { expect_false("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=split") +# context("ds.mean::smk::type=split") test_that("mean values [split]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -104,7 +105,7 @@ test_that("mean values [split]", { expect_false("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=both") +# context("ds.mean::smk::type=both") test_that("mean values [both]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -153,7 +154,7 @@ test_that("mean values [both]", { expect_false("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=combine,save.mean.Nvalid=TRUE") +# context("ds.mean::smk::type=combine,save.mean.Nvalid=TRUE") test_that("mean values [combine]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -189,7 +190,7 @@ test_that("mean values [combine]", { expect_true("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=split,save.mean.Nvalid=TRUE") +# context("ds.mean::smk::type=split,save.mean.Nvalid=TRUE") test_that("mean values [split]", { ds.rm("mean.all.studies") ds.rm("mean.study.specific") @@ -233,7 +234,7 @@ test_that("mean values [split]", { expect_true("Nvalid.study.specific" %in% ls.res$sim3$objects.found) }) -context("ds.mean::smk::type=both,save.mean.Nvalid=TRUE") +# context("ds.mean::smk::type=both,save.mean.Nvalid=TRUE") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_TSC', type='both', save.mean.Nvalid=TRUE) @@ -281,7 +282,7 @@ test_that("mean values [both]", { # Done # -context("ds.mean::smk::shutdown") +# context("ds.mean::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "mean.all.studies", "mean.study.specific", "Nvalid.all.studies", "Nvalid.study.specific")) @@ -289,4 +290,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.mean::smk::done") +# context("ds.mean::smk::done") diff --git a/tests/testthat/test-smk-ds.meanByClass.R b/tests/testthat/test-smk-ds.meanByClass.R index a9d1ef7c4..2c5aba86a 100644 --- a/tests/testthat/test-smk-ds.meanByClass.R +++ b/tests/testthat/test-smk-ds.meanByClass.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.meanByClass::smk::setup") +# context("ds.meanByClass::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC","LAB_HDL","PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.meanByClass::smk::LAB_TSC across PM_BMI_CATEGORICAL categories where both vectors are 'loose'") +# context("ds.meanByClass::smk::LAB_TSC across PM_BMI_CATEGORICAL categories where both vectors are 'loose'") ds.assign("D$LAB_TSC", "ldl") ds.assign("D$PM_BMI_CATEGORICAL", "pm_bmi") test_that("LAB_TSC_across_", { @@ -39,7 +40,7 @@ test_that("LAB_TSC_across_", { expect_equal(res[[6]], '5.89(1.15)') }) -context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories") +# context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories") res <- ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL') test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { @@ -53,7 +54,7 @@ test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { }) -context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL & LAB_TSC across bmi categories") +# context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL & LAB_TSC across bmi categories") res <- ds.meanByClass(x='D', outvar=c('LAB_HDL','LAB_TSC'), covar=c('PM_BMI_CATEGORICAL')) test_that("LAB_HDL-LAB_TSC_across_PM_BMI_CATEGORICAL", { @@ -77,7 +78,7 @@ test_that("LAB_HDL-LAB_TSC_across_PM_BMI_CATEGORICAL", { # res <- ds.meanByClass(datasources=ds.test_env$connection.opal, x='D', outvar=c('LAB_HDL','LAB_TSC'), covar=c('GENDER','PM_BMI_CATEGORICAL','DIS_DIAB')) -context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories, split") +# context("ds.meanByClass::smk::calculate the mean proportion for LAB_HDL across PM_BMI_CATEGORICAL categories, split") res <- ds.meanByClass(x='D', outvar='LAB_HDL', covar='PM_BMI_CATEGORICAL', type='split') test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { @@ -110,7 +111,7 @@ test_that("LAB_HDL_across_PM_BMI_CATEGORICAL", { # Tear down # -context("ds.meanByClass::smk::shutdown") +# context("ds.meanByClass::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "D.PM_BMI_CATEGORICAL1", "D.PM_BMI_CATEGORICAL2", "D.PM_BMI_CATEGORICAL3", @@ -119,4 +120,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.meanByClass::smk::done") +# context("ds.meanByClass::smk::done") diff --git a/tests/testthat/test-smk-ds.meanSdGp.R b/tests/testthat/test-smk-ds.meanSdGp.R index 45da49e34..14561fd09 100644 --- a/tests/testthat/test-smk-ds.meanSdGp.R +++ b/tests/testthat/test-smk-ds.meanSdGp.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.meanSdGp::smk::setup") +# context("ds.meanSdGp::smk::setup") connect.studies.dataset.survival(list("age.60", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.meanSdGp::smk::type=split") +# context("ds.meanSdGp::smk::type=split") test_that("meanSdGp values [split]", { stat.meanSdGp <- ds.meanSdGp(x='D$age.60', y='D$female', type='split') @@ -38,7 +39,7 @@ test_that("meanSdGp values [split]", { expect_true("numeric" %in% class(stat.meanSdGp$Total_Ntotal)) }) -context("ds.meanSdGp::smk::type=combine") +# context("ds.meanSdGp::smk::type=combine") test_that("meanSdGp values [combine]", { stat.meanSdGp <- ds.meanSdGp(x='D$age.60', y='D$female', type='combine') @@ -52,7 +53,7 @@ test_that("meanSdGp values [combine]", { expect_true("numeric" %in% class(stat.meanSdGp$Total_Ntotal)) }) -context("ds.meanSdGp::smk::type=both") +# context("ds.meanSdGp::smk::type=both") test_that("meanSdGp values [both]", { stat.meanSdGp <- ds.meanSdGp(x='D$age.60', y='D$female', type='both') @@ -70,7 +71,7 @@ test_that("meanSdGp values [both]", { # Done # -context("ds.meanSdGp::smk::shutdown") +# context("ds.meanSdGp::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -78,4 +79,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.meanSdGp::smk::done") +# context("ds.meanSdGp::smk::done") diff --git a/tests/testthat/test-smk-ds.merge.R b/tests/testthat/test-smk-ds.merge.R index 521483eb9..fb58dcf5b 100644 --- a/tests/testthat/test-smk-ds.merge.R +++ b/tests/testthat/test-smk-ds.merge.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.merge::smk::setup") +# context("ds.merge::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "DIS_CVA", "DIS_AMI")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.merge::smk") +# context("ds.merge::smk") test_that("simple test", { spec_vectors_1 <- c('D$LAB_TSC', 'D$LAB_HDL') spec_vectors_2 <- c('D$LAB_TSC', 'D$DIS_AMI') @@ -49,7 +50,7 @@ test_that("simple test", { # Done # -context("ds.merge::smk::shutdown") +# context("ds.merge::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "test_1_df", "test_2_df", "merge_newobj")) @@ -57,4 +58,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.merge::smk::done") +# context("ds.merge::smk::done") diff --git a/tests/testthat/test-smk-ds.message.R b/tests/testthat/test-smk-ds.message.R index ec9675870..bc3572633 100644 --- a/tests/testthat/test-smk-ds.message.R +++ b/tests/testthat/test-smk-ds.message.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("ds.message::smk::setup") +# context("ds.message::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -25,7 +26,7 @@ test_that("setup", { # Tests # -context("ds.message::smk") +# context("ds.message::smk") test_that("not exists - request message", { message.res <- ds.message('Test') @@ -94,7 +95,7 @@ test_that("partial - request message - conn 3", { # # Done # -context("ds.message::smk::shutdown") +# context("ds.message::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "Test")) @@ -102,4 +103,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.message::smk::done") +# context("ds.message::smk::done") diff --git a/tests/testthat/test-smk-ds.metadata.R b/tests/testthat/test-smk-ds.metadata.R index a3f5329af..5acbb2ad6 100644 --- a/tests/testthat/test-smk-ds.metadata.R +++ b/tests/testthat/test-smk-ds.metadata.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.metadata::smk::setup") +# context("ds.metadata::smk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.metadata::smk") +# context("ds.metadata::smk") test_that("data.frame metadata", { res <- ds.metadata(x='D') @@ -113,7 +114,7 @@ test_that("column metadata", { # Tear down # -context("ds.metadata::smk::shutdown") +# context("ds.metadata::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -121,4 +122,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.metadata::smk::done") +# context("ds.metadata::smk::done") diff --git a/tests/testthat/test-smk-ds.mice.R b/tests/testthat/test-smk-ds.mice.R index f1b05121e..19e46f740 100644 --- a/tests/testthat/test-smk-ds.mice.R +++ b/tests/testthat/test-smk-ds.mice.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("ds.mice::smk::setup") +# context("ds.mice::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC","LAB_TRIG","LAB_HDL","LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS","DIS_CVA","MEDI_LPD","DIS_DIAB", @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.mice::smk::imp1") +# context("ds.mice::smk::imp1") test_that("mice, initial imputation", { initialImp <- ds.mice(data="D", m=1, method=NULL, predictorMatrix=NULL, post=NULL, seed="NA", newobj_df='impSet') @@ -60,7 +61,7 @@ test_that("mice, initial imputation", { }) -context("ds.mice::smk::imp2") +# context("ds.mice::smk::imp2") test_that("mice, second imputation", { initialImp <- ds.mice(data="D", m=1, method=NULL, predictorMatrix=NULL, post=NULL, seed="NA", @@ -131,7 +132,7 @@ test_that("mice, second imputation", { # Done # -context("ds.mice::smk::shutdown") +# context("ds.mice::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "impSet.1", "imp_new.1","imp_new.2","imp_new.3","imp_new.4","imp_new.5", @@ -140,4 +141,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.mice::smk::done") +# context("ds.mice::smk::done") diff --git a/tests/testthat/test-smk-ds.names.R b/tests/testthat/test-smk-ds.names.R index 97f3fef9e..e73b7b57c 100644 --- a/tests/testthat/test-smk-ds.names.R +++ b/tests/testthat/test-smk-ds.names.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.names::smk::setup") +# context("ds.names::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "DIS_DIAB", "PM_BMI_CONTINUOUS", "LAB_HDL", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.names::smk") +# context("ds.names::smk") test_that("level_names", { myobjects <- c('D$LAB_TSC', 'D$LAB_HDL') res_list <- ds.list(x=myobjects, newobj='my_newobj') @@ -47,7 +48,7 @@ test_that("level_names", { # Tear down # -context("ds.names::smk::shutdown") +# context("ds.names::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "my_newobj")) @@ -55,4 +56,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.names::smk::done") +# context("ds.names::smk::done") diff --git a/tests/testthat/test-smk-ds.ns.R b/tests/testthat/test-smk-ds.ns.R index a1f66c791..d925aa1e9 100644 --- a/tests/testthat/test-smk-ds.ns.R +++ b/tests/testthat/test-smk-ds.ns.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ns::smk::setup") +# context("ds.ns::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ns::smk::test1") +# context("ds.ns::smk::test1") test_that("ns", { ds.ns(x="D$PM_BMI_CONTINUOUS", knots=c(15,25,35), newobj="nsDS", datasources=ds.test_env$connections) @@ -85,7 +86,7 @@ test_that("ns", { # Done # -context("ds.ns::smk::shutdown") +# context("ds.ns::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "nsDS")) @@ -93,4 +94,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.ns::smk::done") +# context("ds.ns::smk::done") diff --git a/tests/testthat/test-smk-ds.numNA.R b/tests/testthat/test-smk-ds.numNA.R index ed332d7a5..0c71e93f9 100644 --- a/tests/testthat/test-smk-ds.numNA.R +++ b/tests/testthat/test-smk-ds.numNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.numNA::smk::setup") +# context("ds.numNA::smk::setup") connect.studies.dataset.cnsim(list("LAB_HDL", "LAB_TRIG", "DIS_CVA")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.numNA::smk") +# context("ds.numNA::smk") test_that("simple numNA", { res1 <- ds.numNA(x='D$LAB_HDL') @@ -52,7 +53,7 @@ test_that("simple numNA", { # Done # -context("ds.numNA::smk::shutdown") +# context("ds.numNA::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -60,4 +61,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.numNA::smk::done") +# context("ds.numNA::smk::done") diff --git a/tests/testthat/test-smk-ds.qlspline.R b/tests/testthat/test-smk-ds.qlspline.R index 2c55b0d50..e8b89701e 100644 --- a/tests/testthat/test-smk-ds.qlspline.R +++ b/tests/testthat/test-smk-ds.qlspline.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("ds.qlspline::smk::setup") +# context("ds.qlspline::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.qlspline::smk::test1") +# context("ds.qlspline::smk::test1") test_that("qlspline", { ds.qlspline(x="D$PM_BMI_CONTINUOUS", q=4, na.rm=TRUE, newobj="qlsplineDS", datasources=ds.test_env$connections) @@ -76,7 +77,7 @@ test_that("qlspline", { }) -context("ds.qlspline::smk::test2") +# context("ds.qlspline::smk::test2") test_that("qlspline", { ds.qlspline(x="D$PM_BMI_CONTINUOUS", q=c(0.3,0.6), na.rm=TRUE, newobj="qlsplineDS2", datasources=ds.test_env$connections) @@ -130,7 +131,7 @@ test_that("qlspline", { # Done # -context("ds.qlspline::smk::shutdown") +# context("ds.qlspline::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "qlsplineDS", "qlsplineDS2")) @@ -138,4 +139,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.qlspline::smk::done") +# context("ds.qlspline::smk::done") diff --git a/tests/testthat/test-smk-ds.quantileMean.R b/tests/testthat/test-smk-ds.quantileMean.R index 59c5479db..1438fb772 100644 --- a/tests/testthat/test-smk-ds.quantileMean.R +++ b/tests/testthat/test-smk-ds.quantileMean.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.quantileMean::smk::setup") +# context("ds.quantileMean::smk::setup") connect.studies.dataset.cnsim(list('LAB_HDL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.quantileMean::smk::standard") +# context("ds.quantileMean::smk::standard") test_that("quantileMean", { res <- ds.quantileMean(x='D$LAB_HDL') @@ -39,7 +40,7 @@ test_that("quantileMean", { expect_equal(res[[8]], 1.5676188, tolerance = .000001) }) -context("ds.quantileMean::smk::split") +# context("ds.quantileMean::smk::split") test_that("quantileMean_split", { ds.assign("D$LAB_HDL", "hdl") res <- ds.quantileMean(x='hdl', type='split') @@ -78,7 +79,7 @@ test_that("quantileMean_split", { # Tear down # -context("ds.quantileMean::smk::shutdown") +# context("ds.quantileMean::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "hdl")) @@ -86,4 +87,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.quantileMean::smk::done") +# context("ds.quantileMean::smk::done") diff --git a/tests/testthat/test-smk-ds.rBinom.R b/tests/testthat/test-smk-ds.rBinom.R index 000f41833..657466933 100644 --- a/tests/testthat/test-smk-ds.rBinom.R +++ b/tests/testthat/test-smk-ds.rBinom.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rBinom::smk::setup") +# context("ds.rBinom::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rBinom::smk::simple test") +# context("ds.rBinom::smk::simple test") test_that("simple test", { res <- ds.rBinom(samp.size = 50, size = 50, prob = 0.25, newobj = "binom_dist", seed.as.integer = 27) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rBinom::smk::shutdown") +# context("ds.rBinom::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "binom_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rBinom::smk::done") +# context("ds.rBinom::smk::done") diff --git a/tests/testthat/test-smk-ds.rNorm.R b/tests/testthat/test-smk-ds.rNorm.R index 9996db9a8..cc63c1c04 100644 --- a/tests/testthat/test-smk-ds.rNorm.R +++ b/tests/testthat/test-smk-ds.rNorm.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rNorm::smk::setup") +# context("ds.rNorm::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rNorm::smk::simple test") +# context("ds.rNorm::smk::simple test") test_that("simple test", { res <- ds.rNorm(samp.size = 50, mean = 10, sd = 5, newobj = "norm_dist", seed.as.integer = 27, force.output.to.k.decimal.places = 4) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rNorm::smk::shutdown") +# context("ds.rNorm::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "norm_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rNorm::smk::done") +# context("ds.rNorm::smk::done") diff --git a/tests/testthat/test-smk-ds.rPois.R b/tests/testthat/test-smk-ds.rPois.R index 38ebe55c2..68e74802c 100644 --- a/tests/testthat/test-smk-ds.rPois.R +++ b/tests/testthat/test-smk-ds.rPois.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rPois::smk::setup") +# context("ds.rPois::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rPois::smk::simple test") +# context("ds.rPois::smk::simple test") test_that("simple test", { res <- ds.rPois(samp.size = 50, lambda = 1, newobj = "pois_dist", seed.as.integer = 27) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rPois::smk::shutdown") +# context("ds.rPois::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "pois_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rPois::smk::done") +# context("ds.rPois::smk::done") diff --git a/tests/testthat/test-smk-ds.rUnif.R b/tests/testthat/test-smk-ds.rUnif.R index 3682a0c30..f8fa681bd 100644 --- a/tests/testthat/test-smk-ds.rUnif.R +++ b/tests/testthat/test-smk-ds.rUnif.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rUnif::smk::setup") +# context("ds.rUnif::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rUnif::smk::simple test") +# context("ds.rUnif::smk::simple test") test_that("simple test", { res <- ds.rUnif(samp.size = 50, min = 0, max = 1, newobj = "unif_dist", seed.as.integer = 27, force.output.to.k.decimal.places = 4) @@ -45,7 +46,7 @@ test_that("simple test", { # Done # -context("ds.rUnif::smk::shutdown") +# context("ds.rUnif::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "unif_dist")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rUnif::smk::done") +# context("ds.rUnif::smk::done") diff --git a/tests/testthat/test-smk-ds.ranksSecure.R b/tests/testthat/test-smk-ds.ranksSecure.R index 890ac2633..43720c1f9 100644 --- a/tests/testthat/test-smk-ds.ranksSecure.R +++ b/tests/testthat/test-smk-ds.ranksSecure.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("ds.ranksSecure::smk::setup") +# context("ds.ranksSecure::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ranksSecure::smk::continous, without NAs, all positive") +# context("ds.ranksSecure::smk::continous, without NAs, all positive") test_that("continous, without NAs, all positive", { res.cc <- ds.completeCases("D$LAB_TSC", newobj="CC_LAB_TSC") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -51,7 +52,7 @@ test_that("continous, without NAs, all positive", { expect_true(all(class(res$final.quantile.vector) %in% c('numeric'))) }) -context("ds.ranksSecure::smk::continous, without NAs, with negative") +# context("ds.ranksSecure::smk::continous, without NAs, with negative") test_that("continous, without NAs, with negative", { res.cc <- ds.completeCases("D$LAB_TRIG", newobj="CC_LAB_TRIG") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -78,7 +79,7 @@ test_that("continous, without NAs, with negative", { expect_true(all(class(res$final.quantile.vector) %in% c('numeric'))) }) -context("ds.ranksSecure::smk::continous, with NAs, all positive") +# context("ds.ranksSecure::smk::continous, with NAs, all positive") test_that("continous, with NAs, all positive", { res <- ds.ranksSecure("D$LAB_TSC") @@ -96,7 +97,7 @@ test_that("continous, with NAs, all positive", { expect_true(all(class(res$final.quantile.vector) %in% c('numeric'))) }) -context("ds.ranksSecure::smk::continous, with NAs, with negative") +# context("ds.ranksSecure::smk::continous, with NAs, with negative") test_that("continous, with NAs, with negative", { res <- ds.ranksSecure("D$LAB_TRIG") @@ -119,7 +120,7 @@ test_that("continous, with NAs, with negative", { # Done # -context("ds.ranksSecure::smk::shutdown") +# context("ds.ranksSecure::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "CC_LAB_TSC", "CC_LAB_TRIG", "final.quantile.df", "summary.ranks.df", "testvar.ranks")) @@ -127,4 +128,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.ranksSecure::smk::done") +# context("ds.ranksSecure::smk::done") diff --git a/tests/testthat/test-smk-ds.rbind.R b/tests/testthat/test-smk-ds.rbind.R index 20cc910c7..af01b50e7 100644 --- a/tests/testthat/test-smk-ds.rbind.R +++ b/tests/testthat/test-smk-ds.rbind.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.rbind::smk::setup") +# context("ds.rbind::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rbind::smk") +# context("ds.rbind::smk") test_that("simple test", { res <- ds.rbind(c("D$survtime", "D$time.id", "D$female", "D$age.60"), newobj="rbind_newobj") @@ -42,7 +43,7 @@ test_that("simple test", { # Done # -context("ds.rbind::smk::shutdown") +# context("ds.rbind::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "rbind_newobj")) @@ -50,4 +51,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rbind::smk::done") +# context("ds.rbind::smk::done") diff --git a/tests/testthat/test-smk-ds.reShape.R b/tests/testthat/test-smk-ds.reShape.R index 5b96a861c..2836d20be 100644 --- a/tests/testthat/test-smk-ds.reShape.R +++ b/tests/testthat/test-smk-ds.reShape.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("ds.reShape::smk::setup") +# context("ds.reShape::smk::setup") connect.studies.dataset.survival(list("id", "study.id", "time.id", "cens", "age.60", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.reShape::smk") +# context("ds.reShape::smk") test_that("simplest ds.reShape, wide", { res <- ds.reShape(data.name="D", v.names="age.60", timevar.name="time.id", idvar.name="id", direction="wide", newobj="reshape1_obj") @@ -45,7 +46,7 @@ test_that("simplest ds.reShape, wide", { # Done # -context("ds.reShape::smk::shutdown") +# context("ds.reShape::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "reshape1_obj")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.reShape::smk::done") +# context("ds.reShape::smk::done") diff --git a/tests/testthat/test-smk-ds.recodeLevels.R b/tests/testthat/test-smk-ds.recodeLevels.R index cdc3d7879..3b813074f 100644 --- a/tests/testthat/test-smk-ds.recodeLevels.R +++ b/tests/testthat/test-smk-ds.recodeLevels.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeLevels::smk::setup") +# context("ds.recodeLevels::smk::setup") connect.studies.dataset.cnsim(list("PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeLevels::smk") +# context("ds.recodeLevels::smk") test_that("new levels", { expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL', newCategories=c('normal', 'overweight', 'obesity'), newobj='bmi_new'), "'ds.recodeLevels' is deprecated.\nUse 'ds.recodeValues' instead.", fixed = TRUE) levels <- ds.levels(x='bmi_new') @@ -39,7 +40,7 @@ test_that("new levels", { expect_equal(levels$sim3$Levels, expected) }) -context("ds.recodeLevels::smk::no connections or newobj") +# context("ds.recodeLevels::smk::no connections or newobj") test_that("new levels auto", { expect_warning(ds.recodeLevels(x='D$PM_BMI_CATEGORICAL', newCategories=c('normal', 'overweight', 'obesity')), "'ds.recodeLevels' is deprecated.\nUse 'ds.recodeValues' instead.", fixed = TRUE) levels <- ds.levels(x='PM_BMI_CATEGORICAL_new') @@ -58,7 +59,7 @@ test_that("new levels auto", { # Tear down # -context("ds.recodeLevels::smk::shutdown") +# context("ds.recodeLevels::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "bmi_new", "PM_BMI_CATEGORICAL_new")) @@ -66,4 +67,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeLevels::smk::done") +# context("ds.recodeLevels::smk::done") diff --git a/tests/testthat/test-smk-ds.recodeValues.R b/tests/testthat/test-smk-ds.recodeValues.R index 187ec63d5..a20d4db47 100644 --- a/tests/testthat/test-smk-ds.recodeValues.R +++ b/tests/testthat/test-smk-ds.recodeValues.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk::setup") +# context("ds.recodeValues::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female", "age.60")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk") +# context("ds.recodeValues::smk") test_that("simple test", { res <- ds.recodeValues("D$survtime", values2replace.vector=c(0,1), new.values.vector=c(-10,10), newobj="recodevalues_newobj") @@ -43,7 +44,7 @@ test_that("simple test", { # # Done # -context("ds.recodeValues::smk::shutdown") +# context("ds.recodeValues::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "recodevalues_newobj")) @@ -51,4 +52,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.recodeValues::smk::done") +# context("ds.recodeValues::smk::done") diff --git a/tests/testthat/test-smk-ds.rep-complex.R b/tests/testthat/test-smk-ds.rep-complex.R index 1a42fdbc3..7d86a8266 100644 --- a/tests/testthat/test-smk-ds.rep-complex.R +++ b/tests/testthat/test-smk-ds.rep-complex.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::smk::complex setup") +# context("ds.rep::smk::complex setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rep::smk::complex") +# context("ds.rep::smk::complex") test_that("complex test", { res1 <- ds.rep(x1 = 4, times = 6, length.out = NA, each = 1, source.x1 = "clientside", source.times = "c", source.length.out = NULL, source.each = "c", x1.includes.characters = FALSE, newobj = "rep1.seq") @@ -44,7 +45,7 @@ test_that("complex test", { # Done # -context("ds.rep::smk::complex shutdown") +# context("ds.rep::smk::complex shutdown") test_that("shutdown", { ds_expect_variables(c("D", "rep1.seq", "rep2.seq")) @@ -52,4 +53,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rep::smk::complex done") +# context("ds.rep::smk::complex done") diff --git a/tests/testthat/test-smk-ds.rep.R b/tests/testthat/test-smk-ds.rep.R index c65cba69c..e3819cc76 100644 --- a/tests/testthat/test-smk-ds.rep.R +++ b/tests/testthat/test-smk-ds.rep.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rep::smk::setup") +# context("ds.rep::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rep::smk") +# context("ds.rep::smk") test_that("simple test", { res <- ds.rep("D$survtime") @@ -37,7 +38,7 @@ test_that("simple test", { # Done # -context("ds.rep::smk::shutdown") +# context("ds.rep::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "seq.vect")) @@ -45,4 +46,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rep::smk::done") +# context("ds.rep::smk::done") diff --git a/tests/testthat/test-smk-ds.replaceNA.R b/tests/testthat/test-smk-ds.replaceNA.R index 9aad07feb..04bdfdf45 100644 --- a/tests/testthat/test-smk-ds.replaceNA.R +++ b/tests/testthat/test-smk-ds.replaceNA.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.replaceNA::smk::setup") +# context("ds.replaceNA::smk::setup") connect.studies.dataset.cnsim(list("LAB_HDL", "LAB_TRIG", "DIS_CVA")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.replaceNA::smk") +# context("ds.replaceNA::smk") test_that("simple replaceNA", { res1 <- ds.replaceNA(x='D$LAB_HDL', forNA=c(1.0, 2.0, 3.0), newobj="newobj1") expect_length(res1, 0) @@ -40,7 +41,7 @@ test_that("simple replaceNA", { # Done # -context("ds.replaceNA::smk::shutdown") +# context("ds.replaceNA::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "newobj1", "newobj2", "newobj3")) @@ -48,4 +49,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.replaceNA::smk::done") +# context("ds.replaceNA::smk::done") diff --git a/tests/testthat/test-smk-ds.rm.R b/tests/testthat/test-smk-ds.rm.R index 75be387a5..f13b1dcfd 100644 --- a/tests/testthat/test-smk-ds.rm.R +++ b/tests/testthat/test-smk-ds.rm.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rm::smk::setup") +# context("ds.rm::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rm::smk") +# context("ds.rm::smk") test_that("simple test", { res1 <- ds.rm("nonexistant_object") @@ -67,7 +68,7 @@ test_that("simple test", { expect_equal(res2$survival1$problem.objects, "") }) -context("ds.rm::smk") +# context("ds.rm::smk") test_that("multiple test", { res1 <- ds.rm("nonexistant_object1,nonexistant_object2") @@ -136,7 +137,7 @@ test_that("multiple test", { # Done # -context("ds.rm::smk::shutdown") +# context("ds.rm::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -144,4 +145,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.rm::smk::done") +# context("ds.rm::smk::done") diff --git a/tests/testthat/test-smk-ds.rowColCalc.R b/tests/testthat/test-smk-ds.rowColCalc.R index 002d763db..792bfb5e4 100644 --- a/tests/testthat/test-smk-ds.rowColCalc.R +++ b/tests/testthat/test-smk-ds.rowColCalc.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.rowColCalc::smk::setup") +# context("ds.rowColCalc::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.rowColCalc::smk") +# context("ds.rowColCalc::smk") ds.rowColCalc(x='D', operation="rowSums", newobj="rsum_hdl_tsc") res <- ds.exists('rsum_hdl_tsc') test_that("rowColCalc_exists", { @@ -34,7 +35,7 @@ test_that("rowColCalc_exists", { expect_true(res$sim3) }) -context("ds.rowColCalc::smk::no newobj") +# context("ds.rowColCalc::smk::no newobj") ds.rowColCalc(x='D', operation="rowSums") res <- ds.exists('rowcolcalc.newobj') test_that("rowColCalc_out_exists", { @@ -48,7 +49,7 @@ test_that("rowColCalc_out_exists", { # # Tear down # -context("ds.rowColCalc::smk::shutdown") +# context("ds.rowColCalc::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "rsum_hdl_tsc", "rowcolcalc.newobj")) @@ -56,4 +57,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.rowColCalc::smk::done") +# context("ds.rowColCalc::smk::done") diff --git a/tests/testthat/test-smk-ds.sample.R b/tests/testthat/test-smk-ds.sample.R index 8a251e3bb..797caefaa 100644 --- a/tests/testthat/test-smk-ds.sample.R +++ b/tests/testthat/test-smk-ds.sample.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.sample::smk::setup") +# context("ds.sample::smk::setup") connect.studies.dataset.survival(list("survtime", "time.id", "female")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.sample::smk::test") +# context("ds.sample::smk::test") test_that("simple test", { res1 <- ds.sample(x="D", size=30) @@ -115,7 +116,7 @@ test_that("simple test", { expect_equal(res2_survtime_length$`total length of test.obj$in.sample in all studies combined`, 126) }) -context("ds.sample::smk::test error") +# context("ds.sample::smk::test error") test_that("simple test, error", { expect_error(ds.sample(x="D$survtime", size="30", newobj="no.obj"), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -131,7 +132,7 @@ test_that("simple test, error", { # Done # -context("ds.sample::smk::shutdown") +# context("ds.sample::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "newobj.sample", "test.obj")) @@ -139,4 +140,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.sample::smk::done") +# context("ds.sample::smk::done") diff --git a/tests/testthat/test-smk-ds.seq.R b/tests/testthat/test-smk-ds.seq.R index f44c7e46e..7da50458a 100644 --- a/tests/testthat/test-smk-ds.seq.R +++ b/tests/testthat/test-smk-ds.seq.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("ds.seq::smk::setup") +# context("ds.seq::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.seq::smk") +# context("ds.seq::smk") test_that("simplest ds.seq", { seq.res <- ds.seq(FROM.value.char="1", BY.value.char="1", LENGTH.OUT.value.char="10", ALONG.WITH.name=NULL, newobj="obj1") @@ -45,7 +46,7 @@ test_that("simplest ds.seq", { # Tear down # -context("ds.seq::smk::shutdown") +# context("ds.seq::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "obj1", "obj2")) @@ -53,4 +54,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.seq::smk::done") +# context("ds.seq::smk::done") diff --git a/tests/testthat/test-smk-ds.setSeed.R b/tests/testthat/test-smk-ds.setSeed.R index eadf7fe18..fadeaae9f 100644 --- a/tests/testthat/test-smk-ds.setSeed.R +++ b/tests/testthat/test-smk-ds.setSeed.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("ds.setSeed::smk::setup") +# context("ds.setSeed::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.setSeed::smk") +# context("ds.setSeed::smk") test_that("basic setSeed", { res.setSeed <- ds.setSeed(1234) @@ -43,7 +44,7 @@ test_that("basic setSeed", { # Done # -context("ds.setSeed::smk::shutdown") +# context("ds.setSeed::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -51,4 +52,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.setSeed::smk::done") +# context("ds.setSeed::smk::done") diff --git a/tests/testthat/test-smk-ds.skewness.R b/tests/testthat/test-smk-ds.skewness.R index e607b9a93..d6f7eaec4 100644 --- a/tests/testthat/test-smk-ds.skewness.R +++ b/tests/testthat/test-smk-ds.skewness.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("ds.skewness::smk::setup") +# context("ds.skewness::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS")) @@ -27,7 +27,7 @@ test_that("setup", { # Method 1 -context("ds.skewness::smk::method 1::split") +# context("ds.skewness::smk::method 1::split") test_that("simple skewness, method 1, split, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 1, type='split') @@ -128,7 +128,7 @@ test_that("simple skewness, method 1, split, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 1::combine") +# context("ds.skewness::smk::method 1::combine") test_that("simple skewness, combine, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 1, type='combine') @@ -199,7 +199,7 @@ test_that("simple skewness, method 1, combine, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 1::both") +# context("ds.skewness::smk::method 1::both") test_that("simple skewness, both, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 1, type='both') @@ -342,7 +342,7 @@ test_that("simple skewness, method 1, both, on PM_BMI_CONTINUOUS", { # Method 2 -context("ds.skewness::smk::method 2::split") +# context("ds.skewness::smk::method 2::split") test_that("simple skewness, method 2, split, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 2, type='split') @@ -443,7 +443,7 @@ test_that("simple skewness, method 2, split, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 2::combine") +# context("ds.skewness::smk::method 2::combine") test_that("simple skewness, combine, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 2, type='combine') @@ -514,7 +514,7 @@ test_that("simple skewness, method 2, combine, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 2::both") +# context("ds.skewness::smk::method 2::both") test_that("simple skewness, both, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 2, type='both') @@ -657,7 +657,7 @@ test_that("simple skewness, method 2, both, on PM_BMI_CONTINUOUS", { # Method 3 -context("ds.skewness::smk::method 3::split") +# context("ds.skewness::smk::method 3::split") test_that("simple skewness, method 3, split, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 3, type='split') @@ -758,7 +758,7 @@ test_that("simple skewness, method 3, split, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 3::combine") +# context("ds.skewness::smk::method 3::combine") test_that("simple skewness, combine, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 3, type='combine') @@ -829,7 +829,7 @@ test_that("simple skewness, method 3, combine, on PM_BMI_CONTINUOUS", { expect_equal(skewness.res$ValidityMessage[1], "VALID ANALYSIS") }) -context("ds.skewness::smk::method 3::both") +# context("ds.skewness::smk::method 3::both") test_that("simple skewness, both, on LAB_TSC", { skewness.res <- ds.skewness(x = 'D$LAB_TSC', method = 3, type='both') @@ -974,7 +974,7 @@ test_that("simple skewness, method 3, both, on PM_BMI_CONTINUOUS", { # Done # -context("ds.skewness::smk::shutdown") +# context("ds.skewness::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -982,4 +982,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.skewness::smk::done") +# context("ds.skewness::smk::done") diff --git a/tests/testthat/test-smk-ds.sqrt.R b/tests/testthat/test-smk-ds.sqrt.R index 9c106c736..ccb50c0ca 100644 --- a/tests/testthat/test-smk-ds.sqrt.R +++ b/tests/testthat/test-smk-ds.sqrt.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.sqrt::smk::setup") +# context("ds.sqrt::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.sqrt::smk") +# context("ds.sqrt::smk") test_that("simple c", { res <- ds.sqrt("D$LAB_TSC", newobj = "sqrt.newobj") @@ -50,7 +51,7 @@ test_that("simple c", { # Done # -context("ds.sqrt::smk::shutdown") +# context("ds.sqrt::smk::shutdown") test_that("setup", { ds_expect_variables(c("D", "sqrt.newobj")) @@ -58,4 +59,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.sqrt::smk::done") +# context("ds.sqrt::smk::done") diff --git a/tests/testthat/test-smk-ds.subset.R b/tests/testthat/test-smk-ds.subset.R index 4accdfe5e..88fecdd2d 100644 --- a/tests/testthat/test-smk-ds.subset.R +++ b/tests/testthat/test-smk-ds.subset.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.subset::smk::setup") +# context("ds.subset::smk::setup") connect.studies.dataset.cnsim(list("DIS_DIAB","PM_BMI_CONTINUOUS","LAB_HDL", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns") +# context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns") ds.subset(datasources=ds.test_env$connections, subset='subD', x='D', rows=c(1:50), cols=c(1,2)) res <- ds.exists('subD') test_that("subD_exists", { @@ -34,7 +35,7 @@ test_that("subD_exists", { expect_true(res$sim3) }) -context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns referred to by their names") +# context("ds.subset::smk::generate a subset of the assigned table (by default the table is named 'D') with the first 50 observations and the two first columns referred to by their names") ds.subset(subset='subD2', x='D', rows=c(1:50), cols = c('DIS_DIAB','PM_BMI_CONTINUOUS')) res <- ds.exists('subD2') test_that("subD2_exists", { @@ -44,7 +45,7 @@ test_that("subD2_exists", { expect_true(res$sim3) }) -context("ds.subset::smk::generate a subset of the table D with bmi values greater than or equal to 25.") +# context("ds.subset::smk::generate a subset of the table D with bmi values greater than or equal to 25.") ds.subset(datasources=ds.test_env$connections, subset='subD3', x='D', logical='PM_BMI_CONTINUOUS>=', threshold=25) res <- ds.exists('subD3') test_that("subD3_exists", { @@ -80,7 +81,7 @@ test_that("subD3_exists", { # Tear down # -context("ds.subset::smk::shutdown") +# context("ds.subset::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "subD", "subD2", "subD3")) @@ -88,4 +89,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subset::smk::done") +# context("ds.subset::smk::done") diff --git a/tests/testthat/test-smk-ds.subsetByClass.R b/tests/testthat/test-smk-ds.subsetByClass.R index 95bf16ebf..71420fcbe 100644 --- a/tests/testthat/test-smk-ds.subsetByClass.R +++ b/tests/testthat/test-smk-ds.subsetByClass.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.subsetByClass::smk::setup") +# context("ds.subsetByClass::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.subsetByClass::smk") +# context("ds.subsetByClass::smk") test_that("gender implicit", { res <- ds.subsetByClass(x='D', subsets='subclasses1') @@ -67,7 +68,7 @@ test_that("gender explicit", { # Tear down # -context("ds.subsetByClass::smk::shutdown") +# context("ds.subsetByClass::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "subclasses1", "subclasses2")) @@ -75,4 +76,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.subsetByClass::smk::done") +# context("ds.subsetByClass::smk::done") diff --git a/tests/testthat/test-smk-ds.summary.R b/tests/testthat/test-smk-ds.summary.R index fd39b021c..750c0392d 100644 --- a/tests/testthat/test-smk-ds.summary.R +++ b/tests/testthat/test-smk-ds.summary.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("ds.summary::smk::setup") +# context("ds.summary::smk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_TRIG', 'LAB_HDL', 'LAB_GLUC_ADJUSTED', 'PM_BMI_CONTINUOUS', 'DIS_CVA', 'MEDI_LPD', 'DIS_DIAB', 'DIS_AMI', 'GENDER', 'PM_BMI_CATEGORICAL')) @@ -23,7 +24,7 @@ test_that("setup", { # # Tests # -context("ds.summary::smk::summary of a dataframe variable") +# context("ds.summary::smk::summary of a dataframe variable") test_that("summary_dataframe_variable", { res <- ds.summary(x='D') @@ -42,7 +43,7 @@ test_that("summary_dataframe_variable", { expect_length(res$sim3$`variables held`, 11) }) -context("ds.summary::smk::summary of a numerical variable") +# context("ds.summary::smk::summary of a numerical variable") test_that("summary_numerical_variable", { res <- ds.summary(x='D$LAB_TSC') @@ -51,7 +52,7 @@ test_that("summary_numerical_variable", { expect_equal(res$sim3$`quantiles & mean`[[4]], 5.786) }) -context("ds.summary::smk::summary of a character variable") +# context("ds.summary::smk::summary of a character variable") test_that("summary_character_variable", { ds.asCharacter(x='D$GENDER', newobj="a_character") res <- ds.summary(x='a_character') @@ -60,7 +61,7 @@ test_that("summary_character_variable", { expect_equal(res$sim2$length, 3088) }) -context("ds.summary::smk::summary of a factor variable") +# context("ds.summary::smk::summary of a factor variable") test_that("summary_factor_variable", { ds.asFactor('D$PM_BMI_CATEGORICAL', newobj="a_factor") res <- ds.summary(x='a_factor') @@ -89,7 +90,7 @@ test_that("summary_factor_variable", { expect_equal(res$sim3$`count of '3'`, 1154) }) -context("ds.summary::smk::summary of a list variable") +# context("ds.summary::smk::summary of a list variable") test_that("summary_list_variable", { ds.asList(x.name='D$PM_BMI_CATEGORICAL', newobj="a_list") res <- ds.summary(x='a_list') @@ -106,7 +107,7 @@ test_that("summary_list_variable", { expect_equal(res$sim3$length, 4128) }) -context("ds.summary::smk::summary of a data frame") +# context("ds.summary::smk::summary of a data frame") test_that("summary_data_frame", { res <- ds.summary(x='D') @@ -122,7 +123,7 @@ test_that("summary_data_frame", { # Tear down # -context("ds.summary::smk::teardown") +# context("ds.summary::smk::teardown") test_that("shutdown", { ds_expect_variables(c("D", "a_character", "a_factor", "a_list")) @@ -130,4 +131,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.summary::smk::done") +# context("ds.summary::smk::done") diff --git a/tests/testthat/test-smk-ds.table.R b/tests/testthat/test-smk-ds.table.R index bae8aae42..0dd48cef1 100644 --- a/tests/testthat/test-smk-ds.table.R +++ b/tests/testthat/test-smk-ds.table.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 @@ # # Set up # -context("ds.table::smk::setup") +# context("ds.table::smk::setup") connect.all.datasets() @@ -23,7 +24,7 @@ test_that("setup", { # Tests # -context("ds.table::smk::dataframe setup") +# context("ds.table::smk::dataframe setup") test_that("simple dataframe input setup", { ds.asFactor(input.var.name="D$FACTOR_CHARACTER", newobj.name="factorCharacter") ds.asFactor(input.var.name="D$FACTOR_INTEGER", newobj.name="factorInteger") @@ -38,7 +39,7 @@ test_that("simple dataframe input setup", { expect_equal(subset.res$validity.check, " appears valid in all sources") }) -context("ds.table::smk::simple table 1D") +# context("ds.table::smk::simple table 1D") test_that("simple table 1D", { table1.res <- ds.table(rvar='tablesource_subset$factorCharacter') @@ -53,7 +54,7 @@ test_that("simple table 1D", { expect_equal(table1.res$validity.message, "Data in all studies were valid") }) -context("ds.table::smk::simple table 2D") +# context("ds.table::smk::simple table 2D") test_that("simple table 2D", { table1.res <- ds.table(rvar='tablesource_subset$factorInteger', cvar='tablesource_subset$factorCharacter') @@ -75,7 +76,7 @@ test_that("simple table 2D", { expect_equal(table1.res$validity.message, "Data in all studies were valid") }) -context("ds.table::smk::simple table 3D") +# context("ds.table::smk::simple table 3D") test_that("simple table 3D", { expect_error(ds.table(rvar='tablesource_subset$factorInteger', cvar='tablesource_subset$factorCharacter', stvar='tablesource_subset$factorCategory'), "There are some DataSHIELD errors, list them with datashield.errors()", fixed = TRUE) @@ -141,7 +142,7 @@ test_that("simple table 3D, with assign", { # Done # -context("ds.table::smk::shutdown") +# context("ds.table::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "factorCharacter", "factorInteger", "factorCategory", "tablesource", "tablesource_subset", "new_table1", "new_table2", "new_table3")) @@ -149,4 +150,4 @@ test_that("shutdown", { disconnect.all.datasets() -context("ds.table::smk::done") +# context("ds.table::smk::done") diff --git a/tests/testthat/test-smk-ds.table1D.R b/tests/testthat/test-smk-ds.table1D.R index 013cdf322..a875f5929 100644 --- a/tests/testthat/test-smk-ds.table1D.R +++ b/tests/testthat/test-smk-ds.table1D.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.table1D::smk::setup") +# context("ds.table1D::smk::setup") connect.studies.dataset.cnsim(list("DIS_CVA","GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables") +# context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables") test_that("GENDER_normal", { res <- expect_warning(ds.table1D(x='D$GENDER'), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -33,7 +34,7 @@ test_that("GENDER_normal", { expect_equal(res$counts[3], 9379) }) -context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail") +# context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail") test_that("DIS_CVA_invalid", { res <- expect_warning(ds.table1D(x='D$DIS_CVA'), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -45,7 +46,7 @@ test_that("DIS_CVA_invalid", { expect_equal(res$validity, "All tables are valid!") }) -context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail split") +# context("ds.table1D::smk::generate a one dimensional table, outputting combined contingency tables fail split") test_that("DIS_CVA_invalid_split", { res <- expect_warning(ds.table1D(x='D$DIS_CVA', type="split"), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -57,7 +58,7 @@ test_that("DIS_CVA_invalid_split", { expect_equal(res$validity, "All tables are valid!") }) -context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables") +# context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables") test_that("GENDER_split", { res <- expect_warning(ds.table1D(x='D$GENDER', type="split"), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -67,7 +68,7 @@ test_that("GENDER_split", { expect_equal(res$counts$sim3[1], 2091) }) -context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables for study 1 and 2") +# context("ds.table1D::smk::generate a one dimensional table, outputting study specific contingency tables for study 1 and 2") test_that("GENDER_split_12", { res <- expect_warning(ds.table1D(datasources=ds.test_env$connections[1:2], x='D$GENDER', type="split"), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -77,7 +78,7 @@ test_that("GENDER_split_12", { expect_equal(res$counts$sim3[1], NULL) }) -context("ds.table1D::smk::generate a one dimensional table, outputting study specific and combined contingency tables") +# context("ds.table1D::smk::generate a one dimensional table, outputting study specific and combined contingency tables") test_that("GENDER_normal_2", { res <- expect_warning(ds.table1D(datasources=ds.test_env$connections, x='D$GENDER'), "'ds.table1D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -90,7 +91,7 @@ test_that("GENDER_normal_2", { # Tear down # -context("ds.table1D::smk::shutdown") +# context("ds.table1D::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -98,4 +99,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.table1D::smk::done") +# context("ds.table1D::smk::done") diff --git a/tests/testthat/test-smk-ds.table2D.R b/tests/testthat/test-smk-ds.table2D.R index 09fc859ce..596ae5080 100644 --- a/tests/testthat/test-smk-ds.table2D.R +++ b/tests/testthat/test-smk-ds.table2D.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("ds.table2D::smk::setup") +# context("ds.table2D::smk::setup") connect.studies.dataset.cnsim(list("DIS_DIAB", "GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.table2D::smk") +# context("ds.table2D::smk") test_that("simple table2D", { table2D.res <- expect_warning(ds.table2D(x='D$DIS_DIAB', y='D$GENDER'), "'ds.table2D' is deprecated.\nUse 'ds.table' instead.", fixed = TRUE) @@ -56,7 +57,7 @@ test_that("simple table2D", { # Done # -context("ds.table2D::smk::shutdown") +# context("ds.table2D::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -64,4 +65,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.table2D::smk::done") +# context("ds.table2D::smk::done") diff --git a/tests/testthat/test-smk-ds.tapply.R b/tests/testthat/test-smk-ds.tapply.R index b79876ff0..67aad82c9 100644 --- a/tests/testthat/test-smk-ds.tapply.R +++ b/tests/testthat/test-smk-ds.tapply.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # Copyright (c) 2014 OBiBa, # 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# 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. @@ -13,7 +14,7 @@ # Set up # -context("ds.tapply::smk::setup") +# context("ds.tapply::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -28,7 +29,7 @@ test_that("setup", { ds.assign('D$LAB_TSC', 'LAB_TSC') ds.assign('D$GENDER', 'GENDER') -context("ds.tapply::smk::fun=mean") +# context("ds.tapply::smk::fun=mean") test_that("simplest 'ds.tapply', fun=mean", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='mean') @@ -56,7 +57,7 @@ test_that("simplest 'ds.tapply', fun=mean", { expect_equal(list$sim3$N[[2]], 1700) }) -context("ds.tapply::smk::fun=sd") +# context("ds.tapply::smk::fun=sd") test_that("simplest 'ds.tapply', fun=sd", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sd') @@ -84,7 +85,7 @@ test_that("simplest 'ds.tapply', fun=sd", { expect_equal(list$sim3$N[[2]], 1700) }) -context("ds.tapply::smk::fun=sum") +# context("ds.tapply::smk::fun=sum") test_that("simplest 'ds.tapply', fun=sum", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sum') @@ -112,7 +113,7 @@ test_that("simplest 'ds.tapply', fun=sum", { expect_equal(list$sim3$N[[2]], 1700) }) -context("ds.tapply::smk::fun=quantile") +# context("ds.tapply::smk::fun=quantile") test_that("simplest 'ds.tapply', fun=quantile", { list <- ds.tapply('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='quantile') @@ -132,7 +133,7 @@ test_that("simplest 'ds.tapply', fun=quantile", { # Tear down # -context("ds.tapply::smk::shutdown") +# context("ds.tapply::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER", "LAB_TSC")) @@ -140,4 +141,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.tapply::smk::done") +# context("ds.tapply::smk::done") diff --git a/tests/testthat/test-smk-ds.tapply.assign.R b/tests/testthat/test-smk-ds.tapply.assign.R index ba13f39df..8fd4918d2 100644 --- a/tests/testthat/test-smk-ds.tapply.assign.R +++ b/tests/testthat/test-smk-ds.tapply.assign.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # Copyright (c) 2014 OBiBa, # 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# 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. @@ -13,7 +14,7 @@ # Set up # -context("ds.tapply.assign::smk::setup") +# context("ds.tapply.assign::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "GENDER")) @@ -28,7 +29,7 @@ test_that("setup", { ds.assign('D$LAB_TSC', 'LAB_TSC') ds.assign('D$GENDER', 'GENDER') -context("ds.tapply.assign::smk::fun=mean") +# context("ds.tapply.assign::smk::fun=mean") test_that("simplest 'ds.tapply.assign', fun=mean", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='mean', newobj="fun_mean.newobj") @@ -44,7 +45,7 @@ test_that("simplest 'ds.tapply.assign', fun=mean", { expect_equal(res.length$`total length of fun_mean.newobj in all studies combined`, 6) }) -context("ds.tapply.assign::smk::fun=sd") +# context("ds.tapply.assign::smk::fun=sd") test_that("simplest 'ds.tapply.assign', fun=sd", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sd', newobj="fun_sd.newobj") @@ -60,7 +61,7 @@ test_that("simplest 'ds.tapply.assign', fun=sd", { expect_equal(res.length$`total length of fun_sd.newobj in all studies combined`, 6) }) -context("ds.tapply.assign::smk::fun=sum") +# context("ds.tapply.assign::smk::fun=sum") test_that("simplest 'ds.tapply.assign', fun=sum", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='sum', newobj="fun_sum.newobj") @@ -76,7 +77,7 @@ test_that("simplest 'ds.tapply.assign', fun=sum", { expect_equal(res.length$`total length of fun_sum.newobj in all studies combined`, 6) }) -context("ds.tapply.assign::smk::fun=quantile") +# context("ds.tapply.assign::smk::fun=quantile") test_that("simplest 'ds.tapply.assign', fun=quantile", { list <- ds.tapply.assign('LAB_TSC', INDEX.names=c('GENDER'), FUN.name='quantile', newobj="fun_quantile.newobj") @@ -96,7 +97,7 @@ test_that("simplest 'ds.tapply.assign', fun=quantile", { # Tear down # -context("ds.tapply.assign::smk::shutdown") +# context("ds.tapply.assign::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER", "LAB_TSC", "fun_mean.newobj", "fun_sd.newobj", "fun_sum.newobj", "fun_quantile.newobj")) @@ -108,4 +109,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.tapply.assign::smk::done") +# context("ds.tapply.assign::smk::done") diff --git a/tests/testthat/test-smk-ds.testObjExists-discordant.R b/tests/testthat/test-smk-ds.testObjExists-discordant.R index a7d89a3ec..5163217fd 100644 --- a/tests/testthat/test-smk-ds.testObjExists-discordant.R +++ b/tests/testthat/test-smk-ds.testObjExists-discordant.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("ds.testObjExists::smk::setup") +# context("ds.testObjExists::smk::setup") connect.discordant.dataset.simple(list("A", "B", "C")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.testObjExists::smk::discordant") +# context("ds.testObjExists::smk::discordant") test_that("simple testObjExists, discordant", { res <- ds.testObjExists('D') @@ -59,7 +60,7 @@ test_that("data.frame testObjExists, discordant", { # Done # -context("ds.testObjExists::smk::shutdown") +# context("ds.testObjExists::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -67,4 +68,4 @@ test_that("shutdown", { disconnect.discordant.dataset.simple() -context("ds.testObjExists::smk::done") +# context("ds.testObjExists::smk::done") diff --git a/tests/testthat/test-smk-ds.testObjExists.R b/tests/testthat/test-smk-ds.testObjExists.R index 5b2b2c383..857fe823c 100644 --- a/tests/testthat/test-smk-ds.testObjExists.R +++ b/tests/testthat/test-smk-ds.testObjExists.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("ds.testObjExists::smk::setup") +# context("ds.testObjExists::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.testObjExists::smk") +# context("ds.testObjExists::smk") test_that("simple testObjExists", { res <- ds.testObjExists('D') @@ -92,7 +93,7 @@ test_that("data.frame testObjExists", { # Done # -context("ds.testObjExists::smk::shutdown") +# context("ds.testObjExists::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "dataframe.newobj")) @@ -100,4 +101,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.testObjExists::smk::done") +# context("ds.testObjExists::smk::done") diff --git a/tests/testthat/test-smk-ds.unList.R b/tests/testthat/test-smk-ds.unList.R index 98fbaa986..806b13315 100644 --- a/tests/testthat/test-smk-ds.unList.R +++ b/tests/testthat/test-smk-ds.unList.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.unList::smk::setup") +# context("ds.unList::smk::setup") connect.studies.dataset.cnsim(list("GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.unList::smk::simple test") +# context("ds.unList::smk::simple test") test_that("simple test", { ds.asList(x.name="D$GENDER", newobj="GENDER.list") @@ -39,7 +40,7 @@ test_that("simple test", { # Done # -context("ds.unList::smk::shutdown") +# context("ds.unList::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER.list", "unlist.newobj")) @@ -47,4 +48,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.unList::smk::done") +# context("ds.unList::smk::done") diff --git a/tests/testthat/test-smk-ds.unique.R b/tests/testthat/test-smk-ds.unique.R index 9aca375ca..21f6f5f03 100644 --- a/tests/testthat/test-smk-ds.unique.R +++ b/tests/testthat/test-smk-ds.unique.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.unique::smk::setup") +# context("ds.unique::smk::setup") connect.studies.dataset.cnsim(list("GENDER")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.unique::smk::simple test") +# context("ds.unique::smk::simple test") test_that("simple test", { original.newobj.length <- ds.length("D$GENDER") @@ -51,7 +52,7 @@ test_that("simple test", { # Done # -context("ds.unique::smk::shutdown") +# context("ds.unique::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "unique.newobj")) @@ -59,4 +60,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.unique::smk::done") +#context("ds.unique::smk::done") diff --git a/tests/testthat/test-smk-ds.var.R b/tests/testthat/test-smk-ds.var.R index bc2aceb6d..834ece232 100644 --- a/tests/testthat/test-smk-ds.var.R +++ b/tests/testthat/test-smk-ds.var.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.var::smk::setup") +# context("ds.var::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.var::smk::split") +# context("ds.var::smk::split") test_that("simple var, split", { var.res <- ds.var(x = 'D$LAB_TSC', type='split') @@ -49,7 +50,7 @@ test_that("simple var, split", { expect_equal(var.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.var::smk::combine") +# context("ds.var::smk::combine") test_that("simple var, combine", { var.res <- ds.var(x = 'D$LAB_TSC', type='combine') @@ -66,7 +67,7 @@ test_that("simple var, combine", { expect_equal(var.res$ValidityMessage[3], "VALID ANALYSIS") }) -context("ds.var::smk::both") +# context("ds.var::smk::both") test_that("simple var, both", { var.res <- ds.var(x = 'D$LAB_TSC', type='both') @@ -100,7 +101,7 @@ test_that("simple var, both", { # Done # -context("ds.var::smk::shutdown") +# context("ds.var::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -108,4 +109,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.var::smk::done") +# context("ds.var::smk::done") diff --git a/tests/testthat/test-smk-ds.vectorCalc.R b/tests/testthat/test-smk-ds.vectorCalc.R index e318c7477..3c03191fe 100644 --- a/tests/testthat/test-smk-ds.vectorCalc.R +++ b/tests/testthat/test-smk-ds.vectorCalc.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.vectorCalc::smk::setup") +# context("ds.vectorCalc::smk::setup") connect.studies.dataset.cnsim(list('LAB_TSC', 'LAB_HDL')) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.vectorCalc::smk") +# context("ds.vectorCalc::smk") test_that("simple test", { vectors <- c('D$LAB_TSC', 'D$LAB_HDL') res <- expect_warning(ds.vectorCalc(x=vectors, calc='+'), "'ds.vectorCalc' is deprecated.\nUse 'ds.make' instead.", fixed = TRUE) @@ -58,7 +59,7 @@ test_that("simple test", { # Done # -context("ds.vectorCalc::smk::shutdown") +# context("ds.vectorCalc::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "vectorcalc.newobj")) @@ -66,4 +67,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.vectorCalc::smk::done") +# context("ds.vectorCalc::smk::done") diff --git a/tests/testthat/test-smk-isDefined.R b/tests/testthat/test-smk-isDefined.R index 5f37b0aa6..ab3f43b07 100644 --- a/tests/testthat/test-smk-isDefined.R +++ b/tests/testthat/test-smk-isDefined.R @@ -1,6 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. -# Copyright (c) 2022 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. @@ -13,7 +13,7 @@ # Set up # -context("isDefined::smk::setup") +# context("isDefined::smk::setup") connect.discordant.dataset.simple(list("A", "B", "C")) @@ -27,7 +27,7 @@ test_that("setup", { # default -context("isDefined::smk::default") +# context("isDefined::smk::default") test_that("default test, dataframe D", { res <- isDefined(ds.test_env$connections, "D") @@ -91,7 +91,7 @@ test_that("default test, dataframe columns D$A,D$B", { # error.message = FALSE -context("isDefined::smk::error.message=FALSE") +# context("isDefined::smk::error.message=FALSE") test_that("error.message=FALSE test, dataframe D", { res <- isDefined(ds.test_env$connections, "D", error.message = FALSE) @@ -197,7 +197,7 @@ test_that("error.message=FALSE test, dataframe columns D$A,D$B", { # error.message = TRUE -context("isDefined::smk::error.message=TRUE") +# context("isDefined::smk::error.message=TRUE") test_that("error.message=TRUE test, dataframe D", { res <- isDefined(ds.test_env$connections, "D", error.message = TRUE) @@ -263,7 +263,7 @@ test_that("error.message=TRUE test, dataframe columns D$A,D$B", { # Done # -context("isDefined::smk::shutdown") +# context("isDefined::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -271,4 +271,4 @@ test_that("shutdown", { disconnect.discordant.dataset.simple() -context("isDefined::smk::done") +# context("isDefined::smk::done") diff --git a/tests/testthat/test-smk_bug-ds.listOpals.R b/tests/testthat/test-smk_bug-ds.listOpals.R index d6b35ff6f..72b28ccdb 100644 --- a/tests/testthat/test-smk_bug-ds.listOpals.R +++ b/tests/testthat/test-smk_bug-ds.listOpals.R @@ -1,6 +1,7 @@ #------------------------------------------------------------------------------- # Copyright (c) 2014 OBiBa, # 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -19,7 +20,7 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL")) # Tests # -context("ds.listOpals::smk::check results") +# context("ds.listOpals::smk::check results") test_that("check results", { message <- "\n* This function lists all Opal objects in the R analysis environment\n\n\n* There is only one set of opals available,\n that is: 'ds.test_env$connections'\n\n\n\n* This set of Opals has been copied to create 'default.opals',\n which all DataSHIELD functions will now use by default.\n If you want to change the default Opal object,\n please run the function ds.setDefaultOpals() again. \n\n\n\n" diff --git a/tests/testthat/test-smk_dgr-ds.asCharacter.R b/tests/testthat/test-smk_dgr-ds.asCharacter.R index 7f9e7c45a..48a2fbd12 100644 --- a/tests/testthat/test-smk_dgr-ds.asCharacter.R +++ b/tests/testthat/test-smk_dgr-ds.asCharacter.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.asCharacter::smk_dgr::setup") +# context("ds.asCharacter::smk_dgr::setup") require(dsDangerClient) @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.asCharacter::smk_dgr::simple test") +# context("ds.asCharacter::smk_dgr::simple test") test_that("simple test", { res <- ds.asCharacter("D$LAB_TSC") @@ -39,7 +40,7 @@ test_that("simple test", { # Shutdown # -context("ds.asCharacter::smk_dgr::stutdown") +# context("ds.asCharacter::smk_dgr::stutdown") test_that("setup", { ds_expect_variables(c("D", "ascharacter.newobj")) @@ -51,4 +52,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.asCharacter::smk_dgr::done") +# context("ds.asCharacter::smk_dgr::done") diff --git a/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.R b/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.R index 52807e3be..64399ac1b 100644 --- a/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.R +++ b/tests/testthat/test-smk_dgr-ds.listClientsideFunctions.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("ds.listClientsideFunctions::smk_dgr::setup") +# context("ds.listClientsideFunctions::smk_dgr::setup") require(dsDangerClient) @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.listClientsideFunctions::smk_dgr::check results") +# context("ds.listClientsideFunctions::smk_dgr::check results") test_that("check results", { output <- list( "ds.DANGERc2sMATDF", @@ -51,7 +52,7 @@ test_that("check results", { # Shutdown # -context("ds.listClientsideFunctions::smk_dgr::shutdown") +# context("ds.listClientsideFunctions::smk_dgr::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -63,4 +64,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.listClientsideFunctions::smk_dgr::done") +# context("ds.listClientsideFunctions::smk_dgr::done") diff --git a/tests/testthat/test-smk_dgr-ds.listServersideFunctions.R b/tests/testthat/test-smk_dgr-ds.listServersideFunctions.R index 27d2e297c..9ed962278 100644 --- a/tests/testthat/test-smk_dgr-ds.listServersideFunctions.R +++ b/tests/testthat/test-smk_dgr-ds.listServersideFunctions.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("ds.listServersideFunctions::smk_dgr::setup") +# context("ds.listServersideFunctions::smk_dgr::setup") require(dsDangerClient) @@ -26,7 +27,7 @@ test_that("setup", { # Tests # -context("ds.listServersideFunctions::smk_dgr::check results") +# context("ds.listServersideFunctions::smk_dgr::check results") test_that("check results", { assign.functions <- factor(c( )) @@ -73,7 +74,7 @@ test_that("check results", { # Done # -context("ds.listServersideFunctions::smk_dgr::shtudown") +# context("ds.listServersideFunctions::smk_dgr::shtudown") test_that("shutdown", { ds_expect_variables(c("D")) @@ -85,4 +86,4 @@ disconnect.studies.dataset.cnsim() # Done # -context("ds.listServersideFunctions::smk_dgr::done") +# context("ds.listServersideFunctions::smk_dgr::done") diff --git a/tests/testthat/test-smk_dgr-ds.recodeValues-factor.R b/tests/testthat/test-smk_dgr-ds.recodeValues-factor.R index 840276726..180278c93 100644 --- a/tests/testthat/test-smk_dgr-ds.recodeValues-factor.R +++ b/tests/testthat/test-smk_dgr-ds.recodeValues-factor.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk_dgr::factor::setup") +# context("ds.recodeValues::smk_dgr::factor::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk_dgr::factor::simple factor 1") +# context("ds.recodeValues::smk_dgr::factor::simple factor 1") test_that("simple factor 1", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c('0'), new.values.vector=c('2'), newobj="GENDER") @@ -79,7 +80,7 @@ test_that("simple factor 1", { expect_length((subset(ndf.sim3, GENDER == 2))$GENDER, 2091) }) -context("ds.recodeValues::smk_dgr::factor::simple factor 2") +# context("ds.recodeValues::smk_dgr::factor::simple factor 2") test_that("simple factor 2", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c(0), new.values.vector=c(2), newobj="GENDER") @@ -134,7 +135,7 @@ test_that("simple factor 2", { expect_length((subset(ndf.sim3, GENDER == 2))$GENDER, 2091) }) -context("ds.recodeValues::smk_dgr::factor::simple factor 3") +# context("ds.recodeValues::smk_dgr::factor::simple factor 3") test_that("simple factor 3", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c(0), new.values.vector=c(2), missing='3', newobj="GENDER") @@ -195,7 +196,7 @@ test_that("simple factor 3", { expect_length((subset(ndf.sim3, GENDER == 3))$GENDER, 0) }) -context("ds.recodeValues::smk_dgr::factor::simple factor 4") +# context("ds.recodeValues::smk_dgr::factor::simple factor 4") test_that("simple factor 4", { res <- ds.recodeValues("D$GENDER", values2replace.vector=c(0,1), new.values.vector=c(10,20), newobj="GENDER") @@ -259,7 +260,7 @@ test_that("simple factor 4", { # # Done # -context("ds.recodeValues::smk_dgr::factor::shutdown") +# context("ds.recodeValues::smk_dgr::factor::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "GENDER", "odf_1", "ndf_1", "odf_2", "ndf_2", "odf_3", "ndf_3", "odf_4", "ndf_4")) @@ -267,4 +268,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeValues::smk_dgr::factor::done") +# context("ds.recodeValues::smk_dgr::factor::done") diff --git a/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.R b/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.R index c6cc808b3..2172c27fd 100644 --- a/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.R +++ b/tests/testthat/test-smk_dgr-ds.recodeValues-factor_missing.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. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk_dgr::factor_missing::setup") +# context("ds.recodeValues::smk_dgr::factor_missing::setup") connect.studies.dataset.cnsim(list("GENDER", "PM_BMI_CATEGORICAL")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 1") +# context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 1") test_that("simple missing factor 1", { res <- ds.recodeValues("D$PM_BMI_CATEGORICAL", values2replace.vector=c(1,2,3), new.values.vector=c(10,20,30), missing='999', newobj="PM_BMI_CATEGORICAL") @@ -109,7 +110,7 @@ test_that("simple missing factor 1", { expect_length((subset(ndf.sim3, PM_BMI_CATEGORICAL == 999))$PM_BMI_CATEGORICAL, 205) }) -context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 2") +# context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 2") test_that("simple missing factor 2", { res <- ds.recodeValues("D$PM_BMI_CATEGORICAL", values2replace.vector=c(1,2), new.values.vector=c(1,2), missing=99, newobj="PM_BMI_CATEGORICAL") @@ -176,7 +177,7 @@ test_that("simple missing factor 2", { expect_length((subset(ndf.sim3, PM_BMI_CATEGORICAL == 99))$PM_BMI_CATEGORICAL, 205) }) -context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 3") +# context("ds.recodeValues::smk_dgr::factor_missing::simple missing factor 3") test_that("simple missing factor 3", { res <- ds.recodeValues("D$PM_BMI_CATEGORICAL", values2replace.vector=c(1,2,3), new.values.vector=c('low','medium','high'), newobj="PM_BMI_CATEGORICAL") @@ -252,7 +253,7 @@ test_that("simple missing factor 3", { # # Done # -context("ds.recodeValues::smk_dgr::factor_missing::shutdown") +# context("ds.recodeValues::smk_dgr::factor_missing::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "PM_BMI_CATEGORICAL", "odf_1", "ndf_1", "odf_2", "ndf_2", "odf_3", "ndf_3")) @@ -260,4 +261,4 @@ test_that("shutdown", { disconnect.studies.dataset.cnsim() -context("ds.recodeValues::smk_dgr::factor_missing::done") +# context("ds.recodeValues::smk_dgr::factor_missing::done") diff --git a/tests/testthat/test-smk_dgr-ds.recodeValues.R b/tests/testthat/test-smk_dgr-ds.recodeValues.R index a7f798210..a7bf78805 100644 --- a/tests/testthat/test-smk_dgr-ds.recodeValues.R +++ b/tests/testthat/test-smk_dgr-ds.recodeValues.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.recodeValues::smk_dgr::setup") +# context("ds.recodeValues::smk_dgr::setup") connect.studies.dataset.survival(list("time.id")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.recodeValues::smk_dgr::simple numeric") +# context("ds.recodeValues::smk_dgr::simple numeric") test_that("simple test", { res <- ds.recodeValues("D$time.id", values2replace.vector=c(1,2), new.values.vector=c(10,20), newobj="time.id") @@ -88,7 +89,7 @@ test_that("simple test", { # # Done # -context("ds.recodeValues::smk_dgr::shutdown") +# context("ds.recodeValues::smk_dgr::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "time.id", "odf", "ndf")) @@ -96,4 +97,4 @@ test_that("shutdown", { disconnect.studies.dataset.survival() -context("ds.recodeValues::smk_dgr::done") +# context("ds.recodeValues::smk_dgr::done") diff --git a/tests/testthat/test-smk_expt-ds.mean.R b/tests/testthat/test-smk_expt-ds.mean.R index 3d1d22fa3..c2682730d 100644 --- a/tests/testthat/test-smk_expt-ds.mean.R +++ b/tests/testthat/test-smk_expt-ds.mean.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. @@ -18,112 +19,112 @@ connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_A # Tests # -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$LAB_TSC',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TSC-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$LAB_TSC', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TSC-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_TSC', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TSC-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { # stat.mean <- ds.mean(x='D$LAB_TRIG',type='combine') # expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TRIG-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { # stat.mean <- ds.mean(x='D$LAB_TRIG', type='split') # expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TRIG-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { # stat.mean <- ds.mean(x='D$LAB_TRIG', type='both') # expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_TRIG-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$LAB_HDL',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_HDL-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$LAB_HDL', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_HDL-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_HDL', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_HDL-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$LAB_GLUC_ADJUSTED',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_GLUC_ADJUSTED-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$LAB_GLUC_ADJUSTED', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_GLUC_ADJUSTED-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$LAB_GLUC_ADJUSTED', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-LAB_GLUC_ADJUSTED-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { stat.mean <- ds.mean(x='D$PM_BMI_CONTINUOUS',type='combine') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CONTINUOUS-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { stat.mean <- ds.mean(x='D$PM_BMI_CONTINUOUS', type='split') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CONTINUOUS-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { stat.mean <- ds.mean(x='D$PM_BMI_CONTINUOUS', type='both') expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CONTINUOUS-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$DIS_CVA", newobj="DIS_CVA") @@ -132,7 +133,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_CVA-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$DIS_CVA", newobj="DIS_CVA") @@ -141,7 +142,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_CVA-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$DIS_CVA", newobj="DIS_CVA") @@ -150,7 +151,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_CVA-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$MEDI_LPD", newobj="MEDI_LPD") @@ -159,7 +160,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-MEDI_LPD-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$MEDI_LPD", newobj="MEDI_LPD") @@ -168,7 +169,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-MEDI_LPD-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$MEDI_LPD", newobj="MEDI_LPD") @@ -177,7 +178,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-MEDI_LPD-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$DIS_DIAB", newobj="DIS_DIAB") @@ -186,7 +187,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_DIAB-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$DIS_DIAB", newobj="DIS_DIAB") @@ -195,7 +196,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_DIAB-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$DIS_DIAB", newobj="DIS_DIAB") @@ -204,7 +205,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_DIAB-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$DIS_AMI", newobj="DIS_AMI") @@ -213,7 +214,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_AMI-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$DIS_AMI", newobj="DIS_AMI") @@ -222,7 +223,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_AMI-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$DIS_AMI", newobj="DIS_AMI") @@ -231,7 +232,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-DIS_AMI-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$GENDER", newobj="GENDER") @@ -240,7 +241,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-GENDER-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$GENDER", newobj="GENDER") @@ -249,7 +250,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-GENDER-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$GENDER", newobj="GENDER") @@ -258,7 +259,7 @@ test_that("mean values [both]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-GENDER-both.rds') }) -context("ds.mean::smk_expt::type=combine") +# context("ds.mean::smk_expt::type=combine") test_that("mean values [combine]", { ds.asNumeric(x.name="D$PM_BMI_CATEGORICAL", newobj="PM_BMI_CATEGORICAL") @@ -267,7 +268,7 @@ test_that("mean values [combine]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CATEGORICAL-combine.rds') }) -context("ds.mean::smk_expt::type=split") +# context("ds.mean::smk_expt::type=split") test_that("mean values [split]", { ds.asNumeric(x.name="D$PM_BMI_CATEGORICAL", newobj="PM_BMI_CATEGORICAL") @@ -276,7 +277,7 @@ test_that("mean values [split]", { expect_equal_to_reference(stat.mean, 'smk_expt-results/ds.mean-PM_BMI_CATEGORICAL-split.rds') }) -context("ds.mean::smk_expt::type=both") +# context("ds.mean::smk_expt::type=both") test_that("mean values [both]", { ds.asNumeric(x.name="D$PM_BMI_CATEGORICAL", newobj="PM_BMI_CATEGORICAL") diff --git a/tests/testthat/test-smk_expt-ds.ranksSecure.R b/tests/testthat/test-smk_expt-ds.ranksSecure.R index 0061df2ce..edb86cd2e 100644 --- a/tests/testthat/test-smk_expt-ds.ranksSecure.R +++ b/tests/testthat/test-smk_expt-ds.ranksSecure.R @@ -1,5 +1,6 @@ #------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -12,7 +13,7 @@ # Set up # -context("ds.ranksSecure::smk_expt::setup") +# context("ds.ranksSecure::smk_expt::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "LAB_TSC")) @@ -24,7 +25,7 @@ test_that("setup", { # Tests # -context("ds.ranksSecure::smk_expt::continous, without NAs, all positive") +# context("ds.ranksSecure::smk_expt::continous, without NAs, all positive") test_that("continous, without NAs, all positive", { res.cc <- ds.completeCases("D$LAB_TSC", newobj="CC_LAB_TSC") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -40,7 +41,7 @@ test_that("continous, without NAs, all positive", { expect_equal_to_reference(res, 'smk_expt-results/ds.ranksSecure-cont.rds') }) -context("ds.ranksSecure::smk_expt::continous, without NAs, with negative") +# context("ds.ranksSecure::smk_expt::continous, without NAs, with negative") test_that("continous, without NAs, with negative", { res.cc <- ds.completeCases("D$LAB_TRIG", newobj="CC_LAB_TRIG") expect_equal(res.cc$validity.check, " appears valid in all sources") @@ -56,14 +57,14 @@ test_that("continous, without NAs, with negative", { expect_equal_to_reference(res, 'smk_expt-results/ds.ranksSecure-cont_neg.rds') }) -context("ds.ranksSecure::smk_expt::continous, with NAs, all positive") +# context("ds.ranksSecure::smk_expt::continous, with NAs, all positive") test_that("continous, with NAs, all positive", { res <- ds.ranksSecure("D$LAB_TSC") expect_equal_to_reference(res, 'smk_expt-results/ds.ranksSecure-cont_nas.rds') }) -context("ds.ranksSecure::smk_expt::continous, with NAs, with negative") +# context("ds.ranksSecure::smk_expt::continous, with NAs, with negative") test_that("continous, with NAs, with negative", { res <- ds.ranksSecure("D$LAB_TRIG") @@ -74,7 +75,7 @@ test_that("continous, with NAs, with negative", { # Done # -context("ds.ranksSecure::smk_expt::shutdown") +# context("ds.ranksSecure::smk_expt::shutdown") test_that("setup", { ds_expect_variables(c("D", "CC_LAB_TSC", "CC_LAB_TRIG", "final.quantile.df", "summary.ranks.df", "testvar.ranks")) @@ -82,4 +83,4 @@ test_that("setup", { disconnect.studies.dataset.cnsim() -context("ds.ranksSecure::smk_expt::done") +# context("ds.ranksSecure::smk_expt::done")