V6.3.5 dev feat/testthat rework

.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$

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

README.md

@@ -23,8 +23,8 @@ And the development version from
 install.packages("remotes")
 remotes::install_github("datashield/dsBaseClient", "<BRANCH>")
 
-# 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,

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

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
 

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
 

tests/testthat/setup.R

@@ -1,18 +1,19 @@
 #-------------------------------------------------------------------------------
 # 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.
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #-------------------------------------------------------------------------------
+
 #
 # 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")

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 <http://www.gnu.org/licenses/>.
 #-------------------------------------------------------------------------------
 
-context("teardown")
+# context("teardown")
 
-context("teardown - done")
+# context("teardown - done")

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")
 

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)

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)
 })

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)
 })

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)

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)
 })

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)
 })

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)
 })

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)
 })

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)
 })

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")
 })

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")

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!")
 })